estimate_motif_from_kmer: Estimate Motif Occurance from Kmers

In TaliaferroLab/FeatureReachR: Extract Enriched Biological Features From RNA-seq Data

Description

Because scanning for PWM matches across both the case and control DNAStringSets can take quite a bit of time, this function estimates matches from a kmer list. We recommend using significantly enriched or depleted kmers as calculated by kmer_compare.

Usage

estimate_motif_from_kmer(
  kmer_list,
  motif_set,
  custom_motif_by_kmer_matrix = NULL
)

Arguments

kmer_list	a character list of kmers
motif_set	one of "CISBPRNA", "RBNS", or "custom"
custom_motif_by_kmer_matrix	NULL unless motif_set = "custom". Use output logical matrix from relate_Kmer_PWM.

Value

a summary table of motif matches in kmers including the pvalue as calculated by phyper, then corrected by p.adjust with the method = "BH".

Examples

enriched_sixmers <- c("AAGGAA", "ACACAC", "AGAAGG", "AGAGAG", "AGAGGG",
"AGGAAG", "AGGAGG", "AGGGAG", "CACACA", "GAAGGA", "GAGAAG", "GAGAGA",
"GAGGAG", "GAGGGA", "GAGGGG", "GGAAGG", "GGAGGA", "GGAGGG", "GGGAGG")
estimate_motif_from_kmer(enriched_sixmers, "RBNS")
estimate_motif_from_kmer(enriched_sixmers, "custom", custom_PWM)

TaliaferroLab/FeatureReachR documentation built on Aug. 15, 2021, 2:21 p.m.