calcMotifEnrichment: Simple inference of motif enrichment for P. hallii

In jtlovell/motifHalliiV2: Analyze motif analysis for P. hallii var. filipes V2

Description

Calculates Motif Enrichment for a vector of P. hallii V2 gene IDs

Usage

calcMotifEnrichment(v2geneID, dropDuplicates = TRUE, verbose = TRUE, FDR.method = "qvalue", ...)

Arguments

v2geneID	A Vector of V2 gene ID e.g. Pahal.J02145
dropDuplicates	Logical, If there are duplicate geneIDs in your list, should they be dropped?
verbose	Logical, should stepwise progress be reported?
FDR.method	If "qvalue", use the qvalue package, any other specification uses p.adjust
...	If FDR.method != "qvalue", specify the parameters of p.adjust

Value

A two element list with the motif enrichment output

enrichmentStats	A dataframe of statistics and annotations for the motifs
enrichmentResults	A PWMEnrich object of enrichment results, can be used for plotting

Examples

library(motifHalliiV2)
library(devtools)

v2geneID<-c("Pahal.J02145", "Pahal.J01516","Pahal.H01249","Pahal.D01315","Pahal.J00094","Pahal.D00330","Pahal.D02670",
"Pahal.D01649", "Pahal.D02828", "Pahal.J00146", "Pahal.C04014", "Pahal.H01253", "Pahal.D00532","Pahal.J00293",
"Pahal.F02021", "Pahal.F02121", "Pahal.F01847", "Pahal.F01958", "Pahal.F00534", "Pahal.B02910")

#no multiple correction
test<-calcMotifEnrichment(v2geneID[1:10], FDR.method="p.adjust", method="none")

#qvalue multiple correction
test<-calcMotifEnrichment(v2geneID[1:10], FDR.method="qvalue")

#bonferroni multiple correction
test<-calcMotifEnrichment(v2geneID[1:10], FDR.method="p.adjust", method="bonferroni")

jtlovell/motifHalliiV2 documentation built on May 20, 2019, 3:14 a.m.