realign_after_collisions: Re-aligns matrices of other quantification types based on the...

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

Description

\lifecycle

experimental This function should be used to keep data consistent among the same analysis: if for some reason you removed the collisions by passing only the sequence count matrix to the remove_collisions function, you should call this function afterwards, providing a list of other quantification matrices. NOTE: if you provided a list of several quantification types to remove_collisions before, there is no need to call this function.

Usage

realign_after_collisions(sc_matrix, other_matrices)

Arguments

sc_matrix	The sequence count matrix already processed for collisions via remove_collisions
other_matrices	A named list of matrices to re-align. Names in the list must be quantification types (quantification_types()) except "seqCount".

Details

For more details on how to use collision removal functionality: vignette("Collision removal functionality", package = "ISAnalytics")

Value

A named list with re-aligned matrices

See Also

remove_collisions

Other Collision removal: remove_collisions()

Examples

op <- options("ISAnalytics.widgets" = FALSE)
path <- 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, root,
    dates_format = "dmy"
)
matrices <- import_parallel_Vispa2Matrices_auto(
    association_file = association_file, root = NULL,
    quantification_type = c("fragmentEstimate", "seqCount"),
    matrix_type = "annotated", workers = 2,
    patterns = NULL, matching_opt = "ANY",
    multi_quant_matrix = FALSE
)
sc_matrix <- remove_collisions(matrices$seqCount, association_file)
others <- matrices[!names(matrices) %in% "seqCount"]
aligned_matrices <- realign_after_collisions(sc_matrix, others)
options(op)

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