write.genes: write gene list from results

In nickfishbane/DMRtools: Tools for 450K differential methylation analysis

Description

writes all the associated genes found in a dmrcate.output object or a top-table generated by limma.tt that satisfy passing a certain threshold

Usage

write.genes(res.obj, file, thresh = 0.05)

Arguments

res.obj	Either a data.frame (limma top-table) with column names "adj.P.Val" and "Gene" or an object of class dmrcate.output created by the dmrcate function in the DMRcate package
file	name (with suggested '.txt' extension) for output of gene list
thresh	Numerical value for p-value cut-off when writing genes from top-table

Details

if res.obj is a dmrcate.output object, it will print all genes with minimum p-value (across probes in the region) less than the supplied threshold. If a threshold is desired, this should be specified in the creation of the object, using pcutoff in the DMRcate::dmrcate() function. If res.obj is a top-table, it will print all gene symbols where the FDR q-value is below the supplied threshold

nickfishbane/DMRtools documentation built on May 23, 2019, 4:47 p.m.