| Type: | Package |
| Title: | Normalize Metabolomic Data using QC Signal |
| Version: | 1.1 |
| Date: | 2021-09-22 |
| Author: | Monica Calderon-Santiago |
| Maintainer: | Monica Calderon-Santiago <b42casam@uco.es> |
| Description: | Takes QC signal for each day and normalize metabolomic data that has been acquired in a certain period of time. At least three QC per day are required. |
| License: | GPL-2 |
| Depends: | R (≥ 3.1.3) |
| Imports: | plyr |
| RoxygenNote: | 5.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2021-09-29 07:56:28 UTC; FQM227 |
| Repository: | CRAN |
| Date/Publication: | 2021-09-29 11:00:06 UTC |
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionLOESS(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionLOESS(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionMultiLOESS(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionMultiLOESS(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionMultiPoly3(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionMultiPoly3(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionMultiPoly4(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionMultiPoly4(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionMultiPoly6(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionMultiPoly6(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionSinglePoly3(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionSinglePoly3(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionSinglePoly4(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionSinglePoly4(LCdata)
## End(Not run)
Generate values for metabolites normalization
Description
According to the area of QC along each day, this function generates values for each sample injected along the day that are going to be used for data normalization.
Usage
QCcorrectionSinglePoly6(LCdata)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected. |
Value
A data set similar to LCdata matrix but with duplicated columns for each compound or entity with the area needed to normalize each of them.
Examples
## Not run:
correctedLCdata<-QCcorrectionSinglePoly6(LCdata)
## End(Not run)
Equation to be used internally to predict values from a regression curve of grade 3
Description
Equation to be used internally to predict values from a regression curve of grade 3
Usage
QCregression(b, c, d, e, x)
Arguments
b |
coefficient from order 0 part of the equation |
c |
coefficient from order 1 part of the equation |
d |
coefficient from order 2 part of the equation |
e |
coefficient from order 3 part of the equation |
x |
the x-axis value from which the y-axis value wanted to be predicted for the equation given by the coefficients |
Value
A y-value calculated for the x-value especified, taking into account the curve described by the coefficients given
Examples
## Not run:
prediction<-QCregression(b,c,d,e,x)
## End(Not run)
#' @export
Equation to be used internally to predict values from a regression curve of grade 4
Description
Equation to be used internally to predict values from a regression curve of grade 4
Usage
QCregression4(b, c, d, e, f, x)
Arguments
b |
coefficient from order 0 part of the equation |
c |
coefficient from order 1 part of the equation |
d |
coefficient from order 2 part of the equation |
e |
coefficient from order 3 part of the equation |
f |
coefficient from order 4 part of the equation |
x |
the x-axis value from which the y-axis value wanted to be predicted for the equation given by the coefficients |
Value
A y-value calculated for the x-value especified, taking into account the curve described by the coefficients given
Examples
## Not run:
prediction<-QCregression4(b,c,d,e,f,x)
## End(Not run)
Equation to be used internally to predict values from a regression curve of grade 6
Description
Equation to be used internally to predict values from a regression curve of grade 6
Usage
QCregression6(b, c, d, e, f, g, h, x)
Arguments
b |
coefficient from order 0 part of the equation |
c |
coefficient from order 1 part of the equation |
d |
coefficient from order 2 part of the equation |
e |
coefficient from order 3 part of the equation |
f |
coefficient from order 4 part of the equation |
g |
coefficient from order 5 part of the equation |
h |
coefficient from order 6 part of the equation |
x |
the x-axis value from which the y-axis value wanted to be predicted for the equation given by the coefficients |
Value
A y-value calculated for the x-value especified, taking into account the curve described by the coefficients given
Examples
## Not run:
prediction<-QCregression4(b,c,d,e,f,g,h,x)
## End(Not run)
Representate the compounds area (normalized or not) as a function of their injection order to study trends.
Description
Export graphs for each compound included in LCdata matrix in which the area of the specified compound is represented vs the injection order.
Usage
graphQC(LCdata, g, NameDataSet)
Arguments
LCdata |
Matrix of data obtained (mainly by LC-MS) that included four data columns ("Compound Name","Order","QC","Day") and then one coulm for each compound or entity detected (normalized or not). |
g |
Number of compounds for which the graph should be obtained |
NameDataSet |
A name for the data set that is going to be used for the pdf file name. It must be given in quotes |
Value
Multiple graphs of the compounds area (normalized or not) vs the injection order.
Examples
## Not run:
graphQC(LCdata,3,"datasetName")
## End(Not run)