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 `remove_collisions()`, 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", package = "ISAnalytics")`

### Value

A named list with re-aligned matrices

### See Also

`remove_collisions`

Other Collision removal: `remove_collisions()`

### Examples

    data("integration_matrices", package = "ISAnalytics")
    data("association_file", package = "ISAnalytics")
    separated <- separate_quant_matrices(
        integration_matrices
    )
    no_coll <- remove_collisions(
        x = separated$seqCount,
        association_file = association_file,
        quant_cols = c(seqCount = "Value"),
        report_path = NULL
    )
    realigned <- realign_after_collisions(
        sc_matrix = no_coll,
        other_matrices = list(fragmentEstimate = separated$fragmentEstimate)
    )
    realigned

[Package ISAnalytics version 1.4.3 Index]