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
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.
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", package = "ISAnalytics")
A named list with re-aligned matrices
Other Collision removal:
remove_collisions()
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