| Type: | Package |
| Title: | Case-Control Analysis of Multi-Allelic Loci |
| Version: | 3.0.3 |
| Date: | 2021-11-01 |
| Author: | Derek Pappas <djpappas75@gmail.com>, Steve Mack <Steven.Mack@ucsf.edu>, Jill Hollenbach <Jill.Hollenbach@ucsf.edu> |
| Maintainer: | Steve Mack <Steven.Mack@ucsf.edu> |
| URL: | http://tools.immunogenomics.org/, https://github.com/IgDAWG/BIGDAWG |
| BugReports: | https://github.com/IgDAWG/BIGDAWG/issues |
| Description: | Data sets and functions for chi-squared Hardy-Weinberg and case-control association tests of highly polymorphic genetic data [e.g., human leukocyte antigen (HLA) data]. Performs association tests at multiple levels of polymorphism (haplotype, locus and HLA amino-acids) as described in Pappas DJ, Marin W, Hollenbach JA, Mack SJ (2016) <doi:10.1016/j.humimm.2015.12.006>. Combines rare variants to a common class to account for sparse cells in tables as described by Hollenbach JA, Mack SJ, Thomson G, Gourraud PA (2012) <doi:10.1007/978-1-61779-842-9_14>. |
| License: | GPL (≥ 3) |
| Depends: | R (≥ 3.5.0) |
| Imports: | XML, httr, haplo.stats, parallel |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.1.2 |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2021-11-16 16:53:55 UTC; derek |
| Repository: | CRAN |
| Date/Publication: | 2021-11-17 11:50:14 UTC |
Amino Acid Analysis Function
Description
This is the workhorse function for the amino acid analysis.
Usage
A(Locus, loci.ColNames, genos, grp, Strict.Bin, ExonAlign, Cores)
Arguments
Locus |
Locus being analyzed. |
loci.ColNames |
The column names of the loci being analyzed. |
genos |
Genotype table. |
grp |
Case/Control or Phenotype groupings. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test. |
ExonAlign |
Exon protein alignment filtered for locus. |
Cores |
Number of cores to use for analysis. |
Note
This function is for internal BIGDAWG use only.
Amino Acid Wrapper
Description
Wrapper function for amino acid analysis.
Usage
A.wrapper(
loci,
loci.ColNames,
genos,
grp,
Exon,
EPL,
Cores,
Strict.Bin,
Output,
Verbose
)
Arguments
loci |
Loci being analyzed. |
loci.ColNames |
The column names of the loci being analyzed. |
genos |
Genotype table. |
grp |
Case/Control or Phenotype groupings. |
Exon |
Exon(s)for targeted analysis. |
EPL |
Protein Alignment List. |
Cores |
Number of cores to use for analysis. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test |
Output |
Data return carryover from main BIGDAWG function |
Verbose |
Summary display carryover from main BIGDAWG function |
Note
This function is for internal BIGDAWG use only.
Contingency Table Check
Description
Checks amino acid contingency table data frame to ensure required variation exists.
Usage
AA.df.check(x, Strict.Bin)
Arguments
x |
contingency table. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test. |
Note
This function is for internal BIGDAWG use only.
Contingency Table Amino Acid ChiSq Testing
Description
Runs ChiSq test on amino acid contingency table data frames.
Usage
AA.df.cs(x, Strict.Bin)
Arguments
x |
contingency table. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test. |
Note
This function is for internal BIGDAWG use only.
Amino Acid Contingency Table Build
Description
Build Contingency Tables for Amino Acid Analysis.
Usage
AAtable.builder(x, y)
Arguments
x |
Filtered alignmnet list element. |
y |
Phenotype groupings. |
Note
This function is for internal BIGDAWG use only.
Alignment Object Creator
Description
Create Object for Exon Protein Alignments.
Usage
AlignObj.Create(Loci, Release, RefTab)
Arguments
Loci |
Loci to be bundled. |
Release |
IMGT/HLA database release version. |
RefTab |
Data of reference exons used for protein alignment creation. |
Note
This function is for internal BIGDAWG use only.
Updated Alignment Object Creator
Description
Synthesize Object for Exon Protein Alignments.
Usage
AlignObj.Update(Loci, Release, RefTab)
Arguments
Loci |
Loci to be bundled. |
Release |
IMGT/HLA database release version. |
RefTab |
Data of reference exons used for protein alignment creation. |
Note
This function is for internal BIGDAWG use only.
Alignment Filter
Description
Filter Protein Exon Alignment File for Specific Alleles.
Usage
AlignmentFilter(Align, Alleles, Locus)
Arguments
Align |
Protein Alignment Object. |
Alleles |
to be pulled. |
Locus |
Locus to be filtered against. |
Note
This function is for internal BIGDAWG use only.
Append Genetic System Locus Designation to Allele String
Description
Adds genetic system (HLA/KIR) to each allele name
Usage
Append.System(x, df.name)
Arguments
x |
Vector Column genotypes to append |
df.name |
String SystemLocus name for each allele. |
Note
This function is for internal use only.
BIGDAWG Main Wrapper Function
Description
This is the main wrapper function for each analysis.
Usage
BIGDAWG(
Data,
HLA = TRUE,
Run.Tests,
Loci.Set,
Exon,
All.Pairwise = FALSE,
Trim = FALSE,
Res = 2,
EVS.rm = FALSE,
Missing = 2,
Strict.Bin = FALSE,
Cores.Lim = 1L,
Results.Dir,
Return = FALSE,
Output = TRUE,
Merge.Output = FALSE,
Verbose = TRUE
)
Arguments
Data |
Name of the genotype data file. |
HLA |
Logical Indicating whether data is HLA class I/II genotyping data only. |
Run.Tests |
Specifics which tests to run. |
Loci.Set |
Input list defining which loci to use for analyses (combinations permitted). |
Exon |
Numeric Exon(s) for targeted amino acid analysis. |
All.Pairwise |
Logical indicating whether all pairwise loci should be analyzed in haplotype analysis. |
Trim |
Logical indicating if HLA alleles should be trimmed to a set resolution. |
Res |
Numeric setting what desired resolution to trim HLA alleles. |
EVS.rm |
Logical indicating if expression variant suffixes should be removed. |
Missing |
Numeric setting allowable missing data for running analysis (may use "ignore"). |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test. |
Cores.Lim |
Integer setting the number of cores accessible to BIGDAWG (Windows limit is 1 core). |
Results.Dir |
Optional, string of full path directory name for BIGDAWG output. |
Return |
Logical Should analysis results be returned as list. |
Output |
Logical Should analysis results be written to output directory. |
Merge.Output |
Logical Should analysis results be merged into a single file for easy access. |
Verbose |
Logical Should a summary of each analysis be displayed in console. |
Examples
## Not run:
### The following examples use the synthetic data set bundled with BIGDAWG
# Haplotype analysis with no missing genotypes for two loci sets
# Significant haplotype association with phenotype
# BIGDAWG(Data="HLA_data", Run.Tests="H", Missing=0, Loci.Set=list(c("DRB1","DQB1")))
# Hardy-Weinberg and Locus analysis ignoring missing data
# Significant locus associations with phenotype at all but DQB1
# BIGDAWG(Data="HLA_data", Run.Tests="L", Missing="ignore")
# Hardy-Weinberg analysis trimming data to 2-Field resolution with no output to files (console only)
# Significant locus deviation at DQB1
BIGDAWG(Data="HLA_data", Run.Tests="HWE", Trim=TRUE, Res=2, Output=FALSE)
## End(Not run)
Build Output Matrix for GL2Tab Conversion
Description
Initializes output matrix format for GL2Tab conversion
Usage
Build.Matrix(System, Loci)
Arguments
System |
Character Genetic system HLA- or KIR |
Loci |
The loci for header names |
Note
This function is for internal use only.
Check Cores Parameters
Description
Check cores limitation for OS compatibility
Usage
Check.Cores(Cores.Lim, Output)
Arguments
Cores.Lim |
Integer How many cores can be used. |
Output |
Logical Should analysis results be written to output directory. |
Check Data Structure
Description
Check data structure for successful conversion.
Usage
Check.Data(Data, System, Convert)
Arguments
Data |
String Type of output. |
System |
Character Genetic system HLA or KIR |
Convert |
String Direction for conversion. |
Note
This function is for internal use only.
Check Input Parameters
Description
Check input parameters for invalid entries.
Usage
Check.Params(
HLA,
Loci.Set,
Exon,
All.Pairwise,
Trim,
Res,
EVS.rm,
Missing,
Cores.Lim,
Return,
Output,
Merge.Output,
Verbose
)
Arguments
HLA |
Logical indicating whether data is HLA class I/II genotyping data only. |
Loci.Set |
Input list defining which loci to use for analyses (combinations permitted). |
Exon |
Numeric Exon(s) for targeted amino acid analysis. |
All.Pairwise |
Logical indicating whether all pairwise loci should be analyzed in haplotype analysis. |
Trim |
Logical indicating if HLA alleles should be trimmed to a set resolution. |
Res |
Numeric setting what desired resolution to trim HLA alleles. |
EVS.rm |
Logical indicating if expression variant suffixes should be removed. |
Missing |
Numeric setting allowable missing data for running analysis (may use "ignore"). |
Cores.Lim |
Integer setting the number of cores accessible to BIGDAWG (Windows limit is 1 core). |
Return |
Logical Should analysis results be returned as list. |
Output |
Logical Should analysis results be written to output directory. |
Merge.Output |
Logical Should analysis results be merged into a single file for easy access. |
Verbose |
Logical Should a summary of each analysis be displayed in console. |
Note
This function is for internal use only.
Check Input Parameters for GLS conversion
Description
Check input parameters for invalid entries.
Usage
Check.Params.GLS(
Convert,
File.Output,
System,
HZY.Red,
DRB345.Check,
Cores.Lim
)
Arguments
Convert |
String Direction for conversion. |
File.Output |
String Type of output. |
System |
String Genetic system (HLA or KIR) of the data being converted |
HZY.Red |
Logical Reduction of homozygote genotypes to single allele. |
DRB345.Check |
Logical Check DR haplotypes for consistency and flag unusual haplotypes. |
Cores.Lim |
Integer How many cores can be used. |
Note
This function is for internal use only.
HLA Allele Legitimacy Check for Amino Acid Analysis
Description
Checks available alleles against data to ensure complete overlap.
Usage
CheckAlleles(x, y)
Arguments
x |
Exon protein list alignment object. |
y |
Genotypes from data file |
Note
This function is for internal BIGDAWG use only.
HLA Formatting Check for Amino Acid Analysis
Description
Checks data to see if HLA data is properly formatted .
Usage
CheckHLA(x)
Arguments
x |
All columns of HLA genotyping data. |
Note
This function is for internal BIGDAWG use only.
HLA Loci Legitimacy Check for Amino Acid Analysis
Description
Checks available loci against data to ensure complete overlap.
Usage
CheckLoci(x, y)
Arguments
x |
Loci available in exon protein list alignment object. |
y |
Unique column names |
Note
This function is for internal BIGDAWG use only.
Function to Check Release Versions
Description
This updates the protein aligment used in checking HLA loci and alleles as well as in the amino acid analysis.
Usage
CheckRelease(Package = T, Alignment = T, Output = F)
Arguments
Package |
Logical to check for BIGDAWG package versions |
Alignment |
Logical to check the IMGT/HLA database version for the alignment bundled with BIGDAWG. |
Output |
Should any error be written to a file |
Note
Requires active internet connection.
GL String Allele Check
Description
GL String check for allele ambiguity formatting
Usage
CheckString.Allele(x)
Arguments
x |
GL String to check against |
Note
This function is for internal use only.
GL String Locus Check
Description
Check GL string for loci appearing in multiple gene fields.
Usage
CheckString.Locus(x, Loci)
Arguments
x |
GL String to check against |
Loci |
Loci to check |
Note
This function is for internal use only.
Condensing Exon Specific Alignments to Single Dataframe
Description
Combines multiple Exon Specific Alignments into a single Alignment object
Usage
Condense.EPL(EPL.Exon)
Arguments
EPL.Exon |
Exon-Locus Specific Amino Acid Alignment. |
Note
This function is for internal BIGDAWG use only.
Create Empty Table
Description
Creates matrix of NA for no result tables.
Usage
Create.Null.Table(Locus, Names, nr)
Arguments
Locus |
Locus being analyzed. |
Names |
Column names for final matrix. |
nr |
Number of rows. |
Note
This function is for internal BIGDAWG use only.
DRB345 haplotype zygosity wrapper
Description
Checks DR haplotypes for correct zygosity and flags unanticipated haplotypes
Usage
DRB345.Check.Wrapper(Genotype, Loci.DR)
Arguments
Genotype |
Row of data set data frame following DRB345 parsing |
Loci.DR |
DRBx Loci of interest to test for consistency |
Note
This function is for internal use only.
DRB345 haplotype zygosity checker single locus
Description
Checks DR haplotypes for correct zygosity and flags unanticipated haplotypes for a single DRBx
Usage
DRB345.Check.Zygosity(Locus, Genotype)
Arguments
Locus |
Locus of interest to test for consistency |
Genotype |
Row of data set data frame following DRB345 parsing |
Note
This function is for internal use only.
DRB345 Expected
Description
Checks DRB1 Genotype and Returns Expected DR345 Loci
Usage
DRB345.Exp(DRB1.Genotype)
Arguments
DRB1.Genotype |
DRB1 Subject Genotypes |
Note
This function is for internal use only.
DRB345 Column Processing
Description
Separates DRB345 column pair into separate columns for each locus
Usage
DRB345.parser(Tab)
Arguments
Tab |
Data frame of sampleIDs, phenotypes, and genotypes |
Note
This function is for internal BIGDAWG use only.
Expression Variant Suffix Removal
Description
Removes expression variant suffixes from HLA alleles in the exon protein alignment object.
Usage
EVSremoval(Locus, EPList)
Arguments
Locus |
Locus to be filtered against. |
EPList |
Exon Protein Alignment Object |
Note
This function is for internal BIGDAWG use only.
Error Code Display and Logging
Description
Displays error codes attributable to data formatting and Locus/Allele naming. Writes to log file.
Usage
Err.Log(Output, x, y = NULL, z = NULL)
Arguments
Output |
Logical indicating if Error logging should be written to a file. |
x |
Log Code. |
y |
Misc information relevant to error. |
z |
Misc information relevant to error. |
Note
This function is for internal BIGDAWG use only.
Filter Exon Specific Alignment Sections
Description
Filters the ExonPtnAlign object by locus and exon.
Usage
Exon.Filter(Locus, Exon, EPL.Locus, RefExons, E.Ptn.Starts)
Arguments
Locus |
Locus being analyzed. |
Exon |
Exon being analyzed. |
EPL.Locus |
ExonPtnAlign object filtered by Locus |
RefExons |
Reference Exon Table |
E.Ptn.Starts |
Exon Protein Overlay Map |
Note
This function is for internal BIGDAWG use only.
Protein Exon Alignment Formatter
Description
Dynamically creates an alignmnet of Allele exons for Analysis.
Usage
ExonPtnAlign.Create(Locus, RefTab)
Arguments
Locus |
Locus alignment to be formatted. |
RefTab |
Reference exon protein information for alignment formatting. |
Note
This function is for internal BIGDAWG use only.
Exon protein alignments.
Description
Alignment object for use in the amino acid analysis.
Usage
ExonPtnList
Format
A list where each element is an alignment dataframe for a single locus.
Replace or Fill 00:00 allele strings
Description
Replaces or Fills absent allele strings.
Usage
Filler(x, Locus = NULL, Type)
Arguments
x |
Genotype |
Locus |
Locus column to adjust. |
Type |
String specifying whether to pad ('Fill') or leave blank ('Remove') absent calls |
Note
This function is for internal use only.
Ambiguous Alleles Locus Name Formatting
Description
Remove or Append Locus name from/to allele in an ambiguous allele string
Usage
Format.Allele(x, Type)
Arguments
x |
Allele String |
Type |
String specifying whether to strip ('off') or append ('on') locus prefix |
Note
This function is for internal use only.
Tabular Data Locus Format Tool
Description
Correctly orders the expanded GL string
Usage
Format.Tab(x, Order)
Arguments
x |
Single row of converted GL string |
Order |
Single row data frame for mapping converted GL strings |
Note
This function is for internal use only.
Locus Ordering for GL2Tab
Description
Orders Locus Calls
Usage
GL2Tab.Loci(Locus, Genotype, System)
Arguments
Locus |
Locus to condense |
Genotype |
Row of loci to condense |
System |
Character Genetic system HLA or KIR |
Note
This function is for internal use only.
Genotype List String Expander
Description
Expands GL string into a table of adjacent loci
Usage
GL2Tab.Sub(x, System)
Arguments
x |
Character GL string to expand |
System |
Character Genetic system HLA or KIR |
Note
This function is for internal use only.
Genotype List String to Tabular Data Conversion
Description
Expands GL strings to columns of adjacent locus pairs.
Usage
GL2Tab.wrapper(df, System, Strip.Prefix, Abs.Fill, Cores)
Arguments
df |
Data frame containing GL strings |
System |
Character Genetic system HLA or KIR |
Strip.Prefix |
Logical Should System/Locus prefixes be stripped from table data. |
Abs.Fill |
Logical Should absent loci special designations be used. |
Cores |
Integer How many cores can be used |
Note
This function is for internal use only
Genotype List String Conversion
Description
Main Workhorse wrapper for cross converting columnar table to GL string representaion.
Usage
GLSconvert(
Data,
Convert,
File.Output = "txt",
System = "HLA",
HZY.Red = FALSE,
DRB345.Check = FALSE,
Strip.Prefix = TRUE,
Abs.Fill = FALSE,
Cores.Lim = 1L
)
Arguments
Data |
String File name or R Data Frame. |
Convert |
String Direction for conversion. |
File.Output |
String Type of File.Output. |
System |
String Genetic system (HLA or KIR) of the data being converted |
HZY.Red |
Logical Reduction of homozygote genotypes to single allele. |
DRB345.Check |
Logical Check DR haplotypes for consistency and flag unusual haplotypes. |
Strip.Prefix |
Logical Should System/Locus prefixes be stripped from table data. |
Abs.Fill |
Logical Should absent loci special designations be used. |
Cores.Lim |
Integer How many cores can be used. |
HLA trimming function
Description
Trim a properly formatted HLA allele to desired number of fields.
Usage
GetField(x, Res)
Arguments
x |
HLA allele. |
Res |
Resolution desired. |
Note
This function is for internal BIGDAWG use only.
File Fetcher
Description
Download Protein Alignment and Accessory Files
Usage
GetFiles(Loci)
Arguments
Loci |
HLA Loci to be fetched. Limited Loci available. |
Note
This function is for internal BIGDAWG use only.
Haplotype Analysis Function for Multicore
Description
This is the workhorse function for the haplotype analysis.
Usage
H.MC(genos.sub, grp, Strict.Bin, Verbose)
Arguments
genos.sub |
The genotype columns of the loci(locus) set being analyzed. |
grp |
Case/Control or Phenotype groupings. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test |
Verbose |
Summary display carryover from main BIGDAWG function |
Note
This function is for internal BIGDAWG use only.
Haplotype Wrapper for Multicore
Description
Wrapper for main H function
Usage
H.MC.wrapper(
SID,
Tabsub,
loci,
loci.ColNames,
genos,
grp,
All.Pairwise,
Strict.Bin,
Output,
Verbose,
Cores
)
Arguments
SID |
Character vector of subject IDs. |
Tabsub |
Data frame of genotype calls for set being analyzed. |
loci |
Character vector of unique loci being analyzed. |
loci.ColNames |
Character vector of genos column names. |
genos |
The genotype columns of the loci set being analyzed. |
grp |
Case/Control or Phenotype groupings. |
All.Pairwise |
Haplotype argument carryover from main BIGDAWG function |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test |
Output |
Data return carryover from main BIGDAWG function |
Verbose |
Summary display carryover from main BIGDAWG function |
Cores |
Cores carryover from main BIGDAWG function |
Note
This function is for internal BIGDAWG use only.
Example HLA Dataset
Description
A synthetic dataset of HLA genotypes for using bigdawg.
Usage
HLA_data
Format
A data frame with 2000 rows and 14 variables
Hardy Weinbergy Equilibrium Function
Description
This is the main function for the HWE analysis.
Usage
HWE(Tab)
Arguments
Tab |
data frame of genotype files post processing. |
Note
This function is for internal BIGDAWG use only.
Hardy Weinbergy Equilibrium Function
Description
This is the workhorse function for each group analysis.
Usage
HWE.ChiSq(genos.sub, loci, nloci)
Arguments
genos.sub |
data frame of genotype files post processing. |
loci |
list of loci. |
nloci |
number of loci in list |
Note
This function is for internal BIGDAWG use only.
Hardy-Weinbery Wrapper
Description
Wrapper for main HWE function
Usage
HWE.wrapper(Tab, Output, Verbose)
Arguments
Tab |
Data frame of genotype files post processing. |
Output |
Data return carryover from main BIGDAWG function |
Verbose |
Summary display carryover from main BIGDAWG function |
Note
This function is for internal BIGDAWG use only.
Locus Analysis Function
Description
This is the workhorse function for the locus level analysis.
Usage
L(loci.ColNames, Locus, genos, grp, Strict.Bin)
Arguments
loci.ColNames |
The column names of the loci being analyzed. |
Locus |
Locus being analyzed. |
genos |
Genotype table |
grp |
Case/Control or Phenotype groupings. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test |
Note
This function is for internal BIGDAWG use only.
Locus Wrapper
Description
Wrapper for main L function
Usage
L.wrapper(nloci, loci, loci.ColNames, genos, grp, Strict.Bin, Output, Verbose)
Arguments
nloci |
Number of loci being analyzed. |
loci |
Loci being analyzed. |
loci.ColNames |
The column names of the loci being analyzed. |
genos |
Genotype table |
grp |
Case/Control or Phenotype groupings. |
Strict.Bin |
Logical specify if strict rare cell binning should be used in ChiSq test |
Output |
Data return carryover from main BIGDAWG function |
Verbose |
Summary display carryover from main BIGDAWG function |
Note
This function is for internal BIGDAWG use only.
Data Object Merge and Output
Description
Whole data set table construction of per haplotype for odds ratio, confidence intervals, and pvalues
Usage
MergeData_Output(BD.out, Run, OutDir)
Arguments
BD.out |
Output of analysis as list. |
Run |
Tests that are to be run as defined by Run.Tests. |
OutDir |
Output directory defined by Results.Dir or default. |
Note
This function is for internal BIGDAWG use only.
HLA P group Finder
Description
Identify P group for a given allele if exists.
Usage
PgrpExtract(x, y)
Arguments
x |
Allele of interest. |
y |
Formatted P groups. |
Note
This function is for internal BIGDAWG use only.
HLA P group File Formatter
Description
Format the hla_nom_p.txt read table object for a specific locus.
Usage
PgrpFormat(x, Locus)
Arguments
x |
P group object from read.table command. |
Locus |
Locus to be filtered on. |
Note
This function is for internal BIGDAWG use only.
Data Summary Function
Description
Summary function for sample population within data file.
Usage
PreCheck(Tab, All.ColNames, rescall, HLA, Verbose, Output)
Arguments
Tab |
Loci available in exon protein list alignment object. |
All.ColNames |
Column names from genotype data. |
rescall |
HLA resolution set for analysis. |
HLA |
HLA BIGDAWG argument passed to function |
Verbose |
Summary display carryover from BIGDAWG function. |
Output |
Data output carryover form BIGDAWG function |
Note
This function is for internal BIGDAWG use only.
Strict Chi-squared Contingency Table Test
Description
Calculates chi-squared contingency table tests and bins all rare cells.
Usage
RunChiSq(x)
Arguments
x |
Contingency table. |
Note
This function is for internal BIGDAWG use only.
Contextual Binning Chi-squared Contingency Table Test
Description
Calculates chi-squared contingency table tests and bins rare cells at 20
Usage
RunChiSq_c(x)
Arguments
x |
Contingency table. |
Note
This function is for internal BIGDAWG use only.
Removes System and Locus from Alleles
Description
Removes the System and Locus designations for alleles calls in GL2Tab
Usage
Stripper(x)
Arguments
x |
Allele |
Note
This function is for internal use only.
Locus Condenser for Tab2GL
Description
Condenses alleles calls of a single locus string using "+"
Usage
Tab2GL.Loci(Locus, Genotype, System, HZY.Red)
Arguments
Locus |
Locus to condense |
Genotype |
Row of loci to condense |
System |
Character Genetic system HLA or KIR |
HZY.Red |
Logical Should homozygote genotypes be a single allele for non-DRB345. |
Note
This function is for internal use only.
Genotype List String Condenser
Description
Condenses column of loci into a GL string using "^"
Usage
Tab2GL.Sub(x, System, HZY.Red)
Arguments
x |
Row of loci to condense |
System |
Character Genetic system HLA or KIR |
HZY.Red |
Logical Should homozygote genotypes be a single allele for non-DRB345. |
Note
This function is for internal use only.
Genotype List String to Tabular Data Conversion
Description
Expands GL strings to columns of adjacent locus pairs.
Usage
Tab2GL.wrapper(df, System, HZY.Red, Abs.Fill, Cores)
Arguments
df |
Data frame containing GL strings |
System |
Character Genetic system HLA or KIR |
HZY.Red |
Logical Should homozygote genotypes be a single allele for non-DRB345. |
Abs.Fill |
Logical Should absent loci special designations be used |
Cores |
Integer How many cores can be used. |
Note
This function is for internal use only.
Table Maker
Description
Table construction of per haplotype for odds ratio, confidence intervals, and pvalues
Usage
TableMaker(x)
Arguments
x |
Contingency table with binned rare cells. |
Note
This function is for internal BIGDAWG use only.
Update function for protein aligment upon new IMGT HLA data release
Description
This updates the protein aligment used in checking HLA loci and alleles as well as in the amino acid analysis.
Usage
UpdateRelease(Force = F, Restore = F, Output = F)
Arguments
Force |
Logical specifiying if update should be forced. |
Restore |
Logical specifying if the original alignment file be restored. |
Output |
Logical indicating if error reporting should be written to file. |
Haplotype Name Builder
Description
Builds table of names for HAPsets
Usage
buildHAPnames(Combn, loci)
Arguments
Combn |
Combination of loci to extraction from genos |
loci |
Character vector of unique loci being analyzed. |
Note
This function is for internal BIGDAWG use only.
Haplotype List Builder
Description
Builds table of haplotypes from combinations
Usage
buildHAPsets(Combn, genos, loci, loci.ColNames)
Arguments
Combn |
Combination of loci to extraction from genos |
genos |
The genotype columns of the loci set being analyzed. |
loci |
Character vector of unique loci being analyzed. |
loci.ColNames |
Character vector of genos column names. |
Note
This function is for internal BIGDAWG use only.
Case-Control Odds ratio calculation and graphing
Description
cci function port epicalc version 2.15.1.0 (Virasakdi Chongsuvivatwong, 2012)
Usage
cci(
caseexp,
controlex,
casenonex,
controlnonex,
cctable = NULL,
graph = TRUE,
design = "cohort",
main,
xlab,
ylab,
xaxis,
yaxis,
alpha = 0.05,
fisher.or = FALSE,
exact.ci.or = TRUE,
decimal = 2
)
Arguments
caseexp |
Number of cases exposed |
controlex |
Number of controls exposed |
casenonex |
Number of cases not exosed |
controlnonex |
Number of controls not exposed |
cctable |
A 2-by-2 table. If specified, will supercede the outcome and exposure variables |
graph |
If TRUE (default), produces an odds ratio plot |
design |
Specification for graph; can be "case control","case-control", "cohort" or "prospective" |
main |
main title of the graph |
xlab |
label on X axis |
ylab |
label on Y axis |
xaxis |
two categories of exposure in graph |
yaxis |
two categories of outcome in graph |
alpha |
level of significance |
fisher.or |
whether odds ratio should be computed by the exact method |
exact.ci.or |
whether confidence limite of the odds ratio should be computed by the exact method |
decimal |
number of decimal places displayed |
Note
This function is for internal BIGDAWG use only.
Case Control Odds Ratio Calculation from Epicalc
Description
Calculates odds ratio and pvalues from 2x2 table
Usage
cci.pval(x)
Arguments
x |
List of 2x2 matrices for calculation, output of TableMaker. |
Note
This function is for internal BIGDAWG use only.
Case Control Odds Ratio Calculation from Epicalc list variation
Description
Variation of the cci.pvalue function
Usage
cci.pval.list(x)
Arguments
x |
List of 2x2 matrices to apply the cci.pvalue function. List output of TableMaker. |
Note
This function is for internal BIGDAWG use only.
Recompute number of alleles
Description
Using Freq.Final, recompute number of alleles
Usage
getAllele.Count(x)
Arguments
x |
Locus specific contingency matrix getCS.Mat output. |
Note
This function is for internal BIGDAWG use only.
Chi square matrices
Description
Chi Square contingency matrix builder with rare cell binning
Usage
getCS.Mat(Locus, genos.sub, Allele.Freq, Allele.Combn)
Arguments
Locus |
Locus of interest. |
genos.sub |
Genotypes for locus of interest. |
Allele.Freq |
Allele frequencies. |
Allele.Combn |
Allele combinations. |
Note
This function is for internal BIGDAWG use only.
Chi square test statistic
Description
Calculate chi square test statistic
Usage
getCS.stat(Locus, Freq.Final)
Arguments
Locus |
Locus of interest. |
Freq.Final |
Contingency Matrix getCS.Mat output. |
Note
This function is for internal BIGDAWG use only.
File Name Extraction
Description
Function to extract file path.
Usage
getFileName(x)
Arguments
x |
File name. |
Note
This function is for internal use only.
Haplotype Table Maker
Description
Builds table of haplotypes
Usage
getHap(SID, HaploEM)
Arguments
SID |
Index number (i.e., row number) of sample ID from genotype matrix. |
HaploEM |
Haplotype output object from haplo.stat::haplo.em function. |
Note
This function is for internal BIGDAWG use only.
Observed Frequency
Description
Get observed frequency of genotypes
Usage
getObsFreq(x, genos.locus)
Arguments
x |
Single genotype. |
genos.locus |
Locus genotypes. |
Note
This function is for internal BIGDAWG use only.
Creation of a 2x2 table using the indicated orientation.
Description
make2x2 function port epicalc version 2.15.1.0 (Virasakdi Chongsuvivatwong, 2012)
Usage
make2x2(caseexp, controlex, casenonex, controlnonex)
Arguments
caseexp |
Number of cases exposed |
controlex |
Number of controls exposed |
casenonex |
Number of cases not exosed |
controlnonex |
Number of controls not exposed |
Note
This function is for internal BIGDAWG use only.
Genotype Combination Maker
Description
Make data frame of possible genotype combinations
Usage
makeComb(x)
Arguments
x |
Number of alleles. |
Note
This function is for internal BIGDAWG use only.
Prepare imported data
Description
Prepare imported data for processing, checks, and analysis.
Usage
prepData(Tab)
Arguments
Tab |
Genotypes dataframe. |
Note
This function is for internal BIGDAWG use only.
Replace absent allele strings
Description
Replaces allowable absent allele strings with ^ symbol.
Usage
rmABstrings(df)
Arguments
df |
Genotypes dataframe. |
Note
This function is for internal BIGDAWG use only.
Haplotype missing Allele summary function
Description
Summary function for identifying missing alleles in a matrix of genotypes.
Usage
summaryGeno.2(geno, miss.val = 0)
Arguments
geno |
Matrix of genotypes. |
miss.val |
Vector of codes for allele missing values. |
Note
This function is for internal BIGDAWG use only and is ported from haplo.stats.