realign_after_collisions {ISAnalytics} | R Documentation |
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.
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()
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)