import_single_Vispa2Matrix: Import a single integration matrix from file

In ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Description

\lifecycle

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, 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
separator	The column delimiter used

Details

The import series of functions is designed to work in combination with the use of Vispa2 pipeline, please refer to this article for more details: VISPA2: A Scalable Pipeline for High-Throughput Identification and Annotation of Vector Integration Sites. For more details on how to properly use these functions, refer to vignette("How to use import functions", package = "ISAnalytics")

Value

A data.table object in tidy format

See Also

Other Import functions: import_association_file(), import_parallel_Vispa2Matrices_auto(), import_parallel_Vispa2Matrices_interactive()

Examples

path_to_file <- system.file("extdata", "ex_annotated_ISMatrix.tsv.xz",
    package = "ISAnalytics"
)
isa_dataframe <- import_single_Vispa2Matrix(path_to_file)

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.