snps_vs_genes_padded: A copy of the above function with padding for species without...

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

A copy of the above function with padding for species without defined UTRs

Description

A copy of the above function with padding for species without defined UTRs

Usage

snps_vs_genes_padded(
  expt,
  snp_result,
  start_col = "start",
  end_col = "end",
  strand_col = "strand",
  padding = 200,
  normalize = TRUE,
  snp_name_col = "seqnames",
  expt_name_col = "chromosome",
  observed_in = NULL,
  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?
strand_col	Define strands.
padding	Add this amount to each CDS.
normalize	Normalize the returns to the length of the putative CDS.
snp_name_col	Name of the column in the metadata with the sequence names.
expt_name_col	Name of the metadata column with the chromosome names.
observed_in	Print some information about how many variants were observed.
ignore_strand	Ignore the 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.