| Title: | Calculates and Analyzes the Proliferative Index |
| Version: | 1.0.1 |
| Description: | Provides functions for calculating and analyzing the proliferative index (PI) from an RNA-seq dataset. As described in Ramaker & Lasseigne, et al. bioRxiv, 2016 <doi:10.1101/063057>. |
| Depends: | R (≥ 3.0.0) |
| Imports: | graphics, stats |
| License: | MIT + file LICENSE |
| LazyData: | true |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| RoxygenNote: | 6.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2018-08-14 17:06:10 UTC; brittany |
| Author: | Brittany Lasseigne [aut, cre], Ryne Ramaker [aut] |
| Maintainer: | Brittany Lasseigne <brittany.lasseigne@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2018-08-14 17:30:03 UTC |
A function for calculating proliferative index from variance stabalized RNA-seq data in the ProliferativeIndex package
Description
This function allows the user to read in data for subsequent proliferative index calculation and analysis
Usage
calculatePI(userObject)
Arguments
userObject |
Output from ProliferativeIndex readDataForPI function |
Examples
calculatePI(exReadDataObj)
A function for comparing proliferative indices from variance stabalized RNA-seq data to model principal componenets in the ProliferativeIndex package
Description
This function allows the user to calculate a correlation between their model and PI
Usage
compareModeltoPI(userObject, vstPI)
Arguments
userObject |
Output from ProliferativeIndex readDataForPI function (user data) |
vstPI |
Output from ProliferativeIndex calculatePI function |
Examples
compareModeltoPI(exReadDataObj, exVSTPI)
A function for comparing proliferative indices from variance stabalized RNA-seq data in the ProliferativeIndex package
Description
This function allows the user to examine a summary and plot of their PIs
Usage
comparePI(vstPIinput)
Arguments
vstPIinput |
Output from ProliferativeIndex calculatePI function (PI of user vst data)//////////////////////////////////////////////////////////////////////// |
Examples
comparePI(exVSTPI)
TCGA ACC data set output from readDataForPI function
Description
This object is the output from readDataForPI taking vstTCGA_ACCData_sub and this model: c("AIFM3", "ATP9B", "CTRC", "MCL1", "MGAT4B", "ODF2L", "SNORA65", "TPPP2")) as inputs.
Usage
data(exReadDataObj)
Format
A list of the vstData (vstTCGA_ACCData_sub data frame with 20501 rows and 10 columns) and the modelIDs (character vector of "AIFM3", "ATP9B", "CTRC", "MCL1", "MGAT4B", "ODF2L", "SNORA65", "TPPP2")
TCGA ACC data set output from calculatePI function
Description
This object is the output from calculatePI from the exReadDataObj as input.
Usage
data(exVSTPI)
Format
A numeric vector of the calculated Proliferation Indices for the vstTCGA_ACCData_sub data
A function for reading data in for use with the ProliferativeIndex package
Description
This function allows the user to read in variance stabalized RNA-seq data and gene model names for subsequent proliferative index calculation and analysis
Usage
readDataForPI(vstData, modelIDs)
Arguments
vstData |
Dataframe of user variance stabalized count data (from DESeq2) with samples in columns and genes in rows. Rownames must be genes. |
modelIDs |
Genes in user identified model for comparison to proliferative index |
Examples
readDataForPI(vstTCGA_ACCData_sub, c("AIFM3", "ATP9B", "CTRC", "MCL1",
"MGAT4B", "ODF2L", "SNORA65", "TPPP2"))
TCGA ACC data set
Description
A dataset containing data from the The Cancer Genome Atlas (TCGA) Adrenocortical Carcinoma (ACC) dataset. This data was obtained from the TCGA data portal (tcga-data.nci.nih.gov) in June 2015. Level 3 RNASeqV2 raw count data was variance stabalized with the DESeq2 v1.8.2 varianceStabilizingTransformation:
Usage
data(vstTCGA_ACCData_sub)
Format
A data frame with 20501 rows and 10 variables