Description Usage Arguments Details Value See Also Examples

View source: R/collision-removal.R

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.

1 | ```
realign_after_collisions(sc_matrix, other_matrices)
``` |

`sc_matrix` |
The sequence count matrix already processed for collisions
via |

`other_matrices` |
A named list of matrices to re-align. Names in the list
must be quantification types ( |

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

A named list with re-aligned matrices

Other Collision removal:
`remove_collisions()`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ```
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)
``` |

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