motif_by_gene: Count Motif occurances within each sequence of a DNAStringSet

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

Description

This function simply returns the number of times a PWM matches with each sequence in a DNAStringSet object.

Usage

motif_by_gene(PWM_list, DNAStringset)

Arguments

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".
DNAStringSet	A DNAStringSet Object. Use readDNAStringSet on a fasta file to create.

Value

a dataframe containing motif counts across each sequences within the DNAStringSet

See Also

write_Sequence, readDNAStringSet, countPWM, motif_compare

Examples

case_fasta <- Biostrings::readDNAStringSet("example_case.fa")

motif_by_gene(CISBPRNA_mm_PWM, case_fasta)
motif_by_gene(RBNS_PWM, case_fasta)

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