relate_kmer_PWM: Relate Kmers and PWM list

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

Description

Create a logical matrix relating position weight matrices to kmers. This creates the input for estimate_motif_from_kmer These matrices take time to make. Logical matrices relating RBNS and CISBPRNA motifs to 4-, 5-, 6- and 7-mers are included within FeatureReachR.

Usage

relate_kmer_PWM(k, PWM_list)

Arguments

k	An integer. Recommended values of K are 3 < k < 8.
PWM_list	a named list of position weight matrices. A list of named matrices where the name is unique, and the matrix columns represent positions, and the rows are the probability of each base "A", "C", "G", and "T". Each column should sum to 1. FeatureReachR has three PWM_lists build in: "CISBPRNA_mm_PWM", "CISBPRNA_hs_PWM", and "RBNS_PWM".

Value

A logial matrix indicating if a motif can match to each kmer.

See Also

countPWM, motif_compare

Examples

#this table is already saved in FeatureReachR
relate_Kmer_PWM(4, RBNS_PWM)
relate_kmer_PWM(6, custom_PWM_list)

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