read_sample_count_files: Read sample count files.

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

Read sample count files.

Description

Reads in individual sample count files to a list of SampleCounts objects.

Usage

read_sample_count_files(
  count_directory = NULL,
  id_column = 1,
  gene_column = 2,
  count_column = 3,
  file_separator = "\t",
  file_header = TRUE,
  strip_ids = FALSE,
  sample_metadata_object = NULL,
  ...
)

Arguments

count_directory	path of directory containing counts.
id_column	the index of column containing unique sgRNA identifiers.
gene_column	the index of column containing gene symbols.
count_column	the index of column containing counts.
file_separator	count file separator.
file_header	whether count file(s) contain a header.
strip_ids	whether to make syntactically valid id names.
sample_metadata_object	a sample metadata object
...	additional read.delim parameters.

Details

Using a list of file names from a SampleMetadata-class object, reads in individual sample counts to SampleCounts-class objects.

Requires three count columns to be defined by their index:

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

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

• count_column - column containing sample counts (Default = 3).

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

Value

a list of SampleCounts objects.

See Also

SampleCounts-class

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