motif_compare: Compare Motif occurances between two DNAStringSets

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

Description

This function compares motif occurances between between case and control DNAStringSets.

Usage

motif_compare(PWM_list, caseDNAStringset, ctrlDNAStringSet)

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

Value

a summary table including the pvalue as calculated by wilcox.test, then corrected by p.adjust with the method = "BH". The mean values for each DNAStringSet, and the log2 fold change between those means.

See Also

write_Sequence, readDNAStringSet, countPWM, motif_by_gene

Examples

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

motif_compare(CISBPRNA_mm_PWM, case_fasta, ctrl_fasta)
motif_compare(RBNS_PWM, case_fasta, ctrl_fasta)

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