read_count_matrix_file: Read in sample count matrix.

In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses

Read in sample count matrix.

Description

Read file containing count matrix into a data frame.

Usage

read_count_matrix_file(
  filepath = NULL,
  file_separator = "\t",
  file_header = TRUE,
  id_column = 1,
  gene_column = 2,
  count_column = NULL,
  processed = FALSE,
  sort_ids = FALSE,
  strip_ids = FALSE,
  ...
)

Arguments

filepath	Character string specifying a file path.
file_separator	count file separator.
file_header	count file header
id_column	the index of column containing unique sgRNA identifiers.
gene_column	the index of column containing gene symbols.
count_column	vector indices of columns containing sample counts.
processed	logical of whether to apply predefined column names.
sort_ids	whether to order by gene and sgRNA identifier (FALSE)
strip_ids	whether to make syntactically valid id names.
...	additional read.delim parameters.

Details

Reads a count matrix file, as defined by filepath, into a data frame. Requires two annotation column indices be defined:

• id_column - column containing guide (sgRNA) identifiers (Default = 1).

• gene_column - column containing gene symbols/identifiers (Default = 2).

• count_column - indices of columns containing sample counts.

There must also be one or more columns containing sample counts whose indices are indicated using count_column. If count_column is NULL then it is assumed that all columns except id_column and gene_column contain count data.

Assumes by default that the count file has a header, as defined by file_header, and that it is tab-delimited, as defined by file_separator.

Value

a data frame containing sample counts.

cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.