snp_subset_genes: Look for only the variant positions in a subset of genes.

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

Look for only the variant positions in a subset of genes.

Description

This was written in response to a query from Nancy and Maria Adelaida who wanted to look only at the variant positions in a few specific genes.

Usage

snp_subset_genes(
  expt,
  snp_expt,
  start_col = "start",
  end_col = "end",
  expt_name_col = "chromosome",
  snp_name_col = "chromosome",
  snp_start_col = "position",
  expt_gid_column = "gid",
  genes = c("LPAL13_120010900", "LPAL13_340013000", "LPAL13_000054100",
    "LPAL13_140006100", "LPAL13_180018500", "LPAL13_320022300")
)

Arguments

expt	Initial expressionset.
snp_expt	Variant position expressionset.
start_col	Metadata column with the start positions for each gene.
end_col	Metadata column with the end of the genes.
expt_name_col	Metadata column with the chromosome names.
snp_name_col	Ditto for the snp_expressionset.
snp_start_col	Metadata column containing the variant positions.
expt_gid_column	ID column for the genes.
genes	Set of genes to cross reference.

Value

New expressionset with only the variants for the genes of interest.

See Also

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

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