DPA {MoonlightR} | R Documentation |
This function carries out the differential phenotypes analysis
DPA(dataType, dataFilt, dataConsortium = "TCGA", fdr.cut = 0.01, logFC.cut = 1, diffmean.cut = 0.25, samplesType, colDescription, gset, gsetFile = "gsetFile.RData")
dataType |
selected |
dataFilt |
obtained from getDataTCGA |
dataConsortium |
is TCGA or GEO, default TCGA |
fdr.cut |
is a threshold to filter DEGs according their p-value corrected |
logFC.cut |
is a threshold to filter DEGs according their logFC |
diffmean.cut |
diffmean.cut for DMR |
samplesType |
samplesType |
colDescription |
colDescription |
gset |
gset |
gsetFile |
gsetFile |
result matrix from differential phenotype analysis
dataDEGs <- DPA(dataFilt = dataFilt, dataType = "Gene expression")