io-RData: Load and extract normalized expression from RData.

In cavei/cellCB: Cell City Band

Load and extract normalized expression from RData.

Description

Load and extract normalized expression from RData.

Load and collect RPKM from RData.

Load and collect DEGs Pvalues with LogFold Change from RData.

Load and collect Active at Days from RData.

Load and collect Active Genes at Days from RData.

Usage

getNormExpressionFromRData(RData, objname)

getRpkmExpressionFromRData(RData, objname)

extractDegsPvaluesWithLFCFromRData(
  RData,
  objname,
  pADJ.thr = 0.05,
  logfcthr = 1.5
)

getDEGsPvaluesFromRData(RData, objname)

getActiveAtDaysFromRData(RData, objname)

Arguments

RData	filnename with RData
objname	the name of the loaded object
pADJ.thr	the threshold for adjusted pvalue, default 0.05
logfcthr	the absolute threshold value for lfc, default 1.5

Value

normalized gene expression matrix

rpkm expression matrix

a three column matix with gene, pvalue and lfc

a list of genes Expressed at a given Day.

a list of genes active at a given Day.

cavei/cellCB documentation built on Sept. 14, 2023, 8:15 a.m.