mitch_import: mitch_import

In markziemann/Mitch: Multi-Contrast Gene Set Enrichment Analysis

mitch_import

Description

This function imports differential omics data from common differential tools like edgeR, limma and DESeq2. It calculates a summarised differential expression metric by multiplying the sign of the log fold change by the -log10 of the p-value. If this behaviour is not desired, mitch_import can be bypassed in favour of another scoring metric.

Usage

mitch_import(x, DEtype, geneIDcol = NULL, geneTable = NULL, joinType = NULL)

Arguments

x	a list of differential expression tables.
DEtype	the program that generated the differential expression table Valid options are 'edgeR', 'DESeq2', 'limma', 'ABSSeq', 'Sleuth', 'Seurat', 'topConfects', 'muscat', 'Swish', 'scDE', 'MAST', 'DEsingle', 'ballgown', 'NOIseq', 'TCC', 'DEDS', 'cuffdiff', 'fishpond', 'missMethyl', 'DMRcate', 'DEP', 'msmsTests', 'plgem', 'SDAMS', 'DEqMS', 'DiffBind' and 'prescored'. Where 'prescored' is a dataframe containing the test statistic and gene ID (either in rowname or separate column) and nothing else. 'preranked' is an alias for 'prescored'.
geneIDcol	the column containing gene names. If gene names are specified as row names, then geneIDcol=NULL.
geneTable	a 2 column table mapping gene identifiers in the profile to gene identifiers in the gene sets.
joinType	the type of join to perform, either 'inner' or 'full'. By default, joins are 'inner' except for Seurat and muscat where full is used.

Value

a multi-column table compatible with mitch_calc analysis.

Examples

# first step is to create a list of differential profiles
data(rna,k9a,k36a)
x<-list('rna'=rna,'k9a'=k9a,'k36a'=k36a)
# import as edgeR table 
imported<-mitch_import(x,DEtype='edger')

markziemann/Mitch documentation built on Nov. 2, 2024, 3:12 a.m.