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

### 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)

[Package ISAnalytics version 1.0.11 Index]