compares: Compare the average Length or GC content of two DNAStringSet...

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

Description

length_compare and GC_compare compare the length and GC content between case and control DNAStringSets respectively.

Usage

length_compare(caseDNAStringSet, ctrlDNAStringSet)

GC_compare(caseDNAStringSet, ctrlDNAStringSet)

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, the mean values for each DNAStringSet, the log2 Fold change between those means, the effect size as calculated by cliff.delta

Functions

• length_compare: the average length of two different DNAStringSet objects and returns a summary statistic table of the comparison.

• GC_compare: the average GC content of two different DNAStringSet objects and returns a summary statistic table of the comparison.

See Also

write_Sequence, readDNAStringSet, letterFrequency, cliff.delta

Examples

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

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