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

realign_after_collisions {ISAnalytics}

R Documentation

Re-aligns matrices of other quantification types based on the processed sequence count matrix.

Description

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

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)

[Package ISAnalytics version 1.0.11 Index]