import_single_Vispa2Matrix {ISAnalytics}R Documentation

Import a single integration matrix from file

Description

[Stable] This function allows to read and import an integration matrix produced as the output of Vispa2 pipeline and converts it to a tidy format.

Usage

import_single_Vispa2Matrix(
  path,
  to_exclude = NULL,
  keep_excluded = FALSE,
  separator = "\t"
)

Arguments

path

The path to the file on disk

to_exclude

Either NULL or a character vector of column names that should be ignored when importing

keep_excluded

Keep the columns in to_exclude as additional id columns?

separator

The column delimiter used, defaults to \t

Details

For more details see the "How to use import functions" vignette: vignette("import_functions_howto", package = "ISAnalytics")

Value

A data.table object in tidy format

See Also

Other Import functions: import_Vispa2_stats(), import_association_file(), import_parallel_Vispa2Matrices()

Examples

fs_path <- system.file("extdata", "fs.zip", package = "ISAnalytics")
fs <- unzip_file_system(fs_path, "fs")
matrix_path <- fs::path(
    fs,
    "PJ01",
    "quantification",
    "POOL01-1",
    "PJ01_POOL01-1_seqCount_matrix.no0.annotated.tsv.gz"
)
matrix <- import_single_Vispa2Matrix(matrix_path)
head(matrix)

[Package ISAnalytics version 1.4.1 Index]