make.fold.change {metaseqR} | R Documentation |
Returns a matrix of fold changes based on the requested
contrast, the list of all samples and the data matrix
which is produced by the metaseqr workflow. For details
on the contrast
, sample.list
and
log.offset
parameters, see the main usage page of
metaseqr. This function is intended mostly for internal
use but can also be used independently.
make.fold.change(contrast, sample.list, data.matrix, log.offset = 1)
contrast |
the vector of requested statistical comparison contrasts. |
sample.list |
the list containing condition names and the samples under each condition. |
data.matrix |
a matrix of gene expression data whose column names are the same as the sample names included in the sample list. |
log.offset |
a number to be added to each element of data matrix in order to avoid Infinity on log type data transformations. |
A matrix of fold change ratios, treatment to control, as these are parsed from contrast.
Panagiotis Moulos
data.matrix <- round(1000*matrix(runif(400),100,4)) rownames(data.matrix) <- paste("gene_",1:100,sep="") colnames(data.matrix) <- c("C1","C2","T1","T2") fc <- make.fold.change("Control_vs_Treatment",list(Control=c("C1","C2"), Treatment=c("T1","T2")),data.matrix)