realign_after_collisions: Re-aligns matrices of other quantification types based on the...

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

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,
  sample_column = pcr_id_column()
)

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".
sample_column	The name of the column containing the sample identifier

Details

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

Value

A named list with re-aligned matrices

See Also

remove_collisions

Other Data cleaning and pre-processing: aggregate_metadata(), aggregate_values_by_key(), compute_near_integrations(), default_meta_agg(), outlier_filter(), outliers_by_pool_fragments(), purity_filter(), remove_collisions(), threshold_filter()

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

calabrialab/ISAnalytics documentation built on Nov. 2, 2023, 8:57 p.m.