snps_intersections: Cross reference observed variants against the transcriptome...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Cross reference observed variants against the transcriptome annotation.

Description

This function should provide counts of how many variant positions were observed with respect to each chromosome and with respect to each annotated sequence (currently this is limited to CDS, but that is negotiable).

Usage

snps_intersections(
  expt,
  snp_result,
  start_column = "start",
  end_column = "end",
  chr_column = "seqnames"
)

Arguments

expt	The original expressionset. This provides the annotation data.
snp_result	The result from get_snp_sets or count_expt_snps.
start_column	Metadata column with the start position of each ORF.
end_column	Metadata column with the end position of each ORF.
chr_column	Column in the annotation with the chromosome names.

Value

List containing the set of intersections in the conditions contained in snp_result, the summary of numbers of variants per chromosome, and

See Also

[snps_vs_genes()] [GenomicRanges::makeGRangesFromDataFrame()] [IRanges::subsetByOverlaps()] [IRanges::countOverlaps()]

Examples

 ## Not run: 
 expt <- create_expt(metadata, gene_information)
 snp_expt <- count_expt_snps(expt)
 snp_result <- get_snp_sets(snp_expt)
 intersections <- snps_vs_intersections(expt, snp_result)

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.