kmer_compare: Compare kmer content between two DNAStringSets

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

Description

This function compares kmer content between between case and control DNAStringSets

Usage

kmer_compare(caseDNAStringSet, ctrlDNAStringSet, k)

Arguments

caseDNAStringSet	A DNAStringSet Object. Use readDNAStringSet on a fasta file to create.
ctrlDNAStringSet	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, oligonucleotideFrequency,kmer_by_gene, cliff.delta

Examples

case_fasta <- Biostrings::readDNAStringSet("example_case.fa")
ctrl_fasta <- Biostrings::readDNAStringSet("example_ctrl.fa")
kmer_compare(case_fasta, ctrl_fasta, 6)

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