snps_vs_genes: Make a summary of the observed snps by gene ID.

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

Make a summary of the observed snps by gene ID.

Description

Instead of cross referencing variant positions against experimental condition, one might be interested in seeing what variants are observed per gene. This function attempts to answer that question.

Usage

snps_vs_genes(
  expt,
  snp_result,
  start_col = "start",
  end_col = "end",
  snp_name_col = "seqnames",
  observed_in = NULL,
  expt_name_col = "chromosome",
  ignore_strand = TRUE
)

Arguments

expt	The original expressionset.
snp_result	The result from get_snp_sets().
start_col	Which column provides the start of each gene?
end_col	and the end column of each gene?
snp_name_col	Name of the column in the metadata with the sequence names.
observed_in	Minimum proportion of samples required before this is deemed real.
expt_name_col	Name of the metadata column with the chromosome names.
ignore_strand	Ignore strand information when returning?

Value

List with some information by gene.

See Also

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

Examples

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

## End(Not run)

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