exprData: Expression data subset

In anabeloff/vic3PCD: Transcriptome analysis of Cryphonectria parasititca allorecognotion

Description

exprDataReturns a list made of count matrix and DESeq2 results data.frame.

Usage

exprData(value = NULL, pvalue = 0.1, ds = NA, shrinkLFC = FALSE, calcDE = TRUE)

Arguments

value	Numeric. LFC threshold to subset dataset based on DESeq2 results values. Taken as absolute value.
pvalue	Numeric. P-value threshhold.
ds	DESeq2 dataset, output of DESeq(x).
shrinkLFC	Logical. Apply lfcShrink function to generate DESeq2 results.
calcDE	Logical. Calcilate differential expression by substracting 'control' from 'expreriment' columns. To work this option requires colData(dds) to contain column called 'clustering'. This column must tag samples as 'control' or 'experiment'.

anabeloff/vic3PCD documentation built on Dec. 2, 2020, 11:03 a.m.