has_consistentSeqlevels: Test consistency of chromosome naming styles (aka seqlevels;...

In fursham-h/factR: Functional Annotation of Custom Transcriptomes

Test consistency of chromosome naming styles (aka seqlevels; e.g. "chr1" vs "1") across multiple objects

Description

This function will determine if all input ranges objects have the same chromosome naming convention. Input objects can be GenomicRanges, BSgenome or Biostrings object with seqlevel information.

Usage

has_consistentSeqlevels(..., verbose = TRUE)

Arguments

...	Two or more objects with seqlevels information
verbose	Whether to print out message

Value

Logical value as to whether all objects have consistent seqlevel styles

Author(s)

Fursham Hamid

Examples

## ---------------------------------------------------------------------
## EXAMPLE USING TOY DATASET
## ---------------------------------------------------------------------
require(GenomicRanges)

## Create toy GRanges objects
gr1 <- GRanges("1", IRanges(start = c(1, 101), width = c(20, 20)), "+")
gr2 <- GRanges("chr1", IRanges(start = c(1, 101), width = c(20, 20)), "+")

## Test for seqlevels consistency
has_consistentSeqlevels(gr1, gr2)

## Input can be a Biostrings object with seqlevels information
x0 <- c("chr2" = "CTCACCAGTAT", "chr3" = "TGTCAGTCGA")
dna <- Biostrings::DNAStringSet(x0)

## Test for seqlevels consistency
has_consistentSeqlevels(gr1, dna)
has_consistentSeqlevels(gr2, dna)

fursham-h/factR documentation built on Aug. 20, 2023, 1:58 p.m.