generate_Vispa2_launch_AF: Creates a reduced association file for Vispa2 run, given...

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

Description

The function selects the appropriate columns and prepares a file for the launch of Vispa2 pipeline for each project/pool pair specified.

Usage

generate_Vispa2_launch_AF(association_file, project, pool, path)

Arguments

association_file	The imported association file (via import_association_file)
project	A vector of characters containing project names
pool	A vector of characters containing pool names. NOTE: the names should refer to the values contained in the PoolID column of the association file and NOT the concatenatePoolIDSeqRun column!
path	A single string representing the path to the folder where files should be written. If the folder doesn't exist it will be created.

Details

Note: the function is vectorized, meaning you can specify more than one project and more than one pool as vectors of characters, but you must ensure that:

• Both project and pool vectors have the same length

• You correclty type names in corresponding positions, for example c("CLOEXP", "PROJECT1100", "PROJECT1100") - c("POOL6", "ABX-LR-PL5-POOL14-1", "ABX-LR-PL6-POOL15-1"). If you type a pool in the position of a corresponding project that doesn't match no file will be produced since that pool doesn't exist in the corresponding project.

Value

returns NULL

See Also

Other Utility functions: as_sparse_matrix(), generate_blank_association_file(), unzip_file_system()

Examples

op <- options("ISAnalytics.widgets" = FALSE)
temp <- tempdir()
path_af <- system.file("extdata", "ex_association_file.tsv",
    package = "ISAnalytics"
)
root_pth <- system.file("extdata", "fs.zip", package = "ISAnalytics")
root <- unzip_file_system(root_pth, "fs")
association_file <- import_association_file(path_af, root,
    dates_format = "dmy"
)
generate_Vispa2_launch_AF(association_file, "CLOEXP", "POOL6", temp)
options(op)

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