grep_gene_expression: Grep the expression values of a gene from a vast-tools output...

In Ni-Ar/niar: Nice Interactive Analysis with R

Grep the expression values of a gene from a vast-tools output table.

Description

Grep the expression values of a gene from a vast-tools output table.

Usage

grep_gene_expression(
  vst_expression_tbl,
  ensembl_gene_id,
  tmp_dir = tempdir(),
  verbose = FALSE,
  clear_tmp = TRUE,
  fast_grep = TRUE
)

Arguments

vst_expression_tbl	Path to a vast-tools expression table (either cRPKM or TPM)
ensembl_gene_id	an ensembl gene id that is used to grep a line
tmp_dir	a temporary directory where to same the intermediate files
verbose	Logical, print some info?
clear_tmp	Logical, remove the temporary files after the function is done?
fast_grep	Logical, if TRUE use 'grep -m1' to stop the search after first match found. If FALSE all vst_expression_tbl is read.

Value

a data.frame

Examples

grep_gene_expression(path_to_vst_Expression_tbl, ensembl_gene_id) |>
    tidy_vst_expr(ID_cols = "ensembl_geneid", expression_unit = "TMP")

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.