Get filter for barcodes based on the number of chains for TRA, TRB, IGL, IGK, and IGH present

Source: R/filter_vdj_chain_count.R

Wrapper around scater::isOutlier, arguments type and nmads refer to the same thing. For mitochondrial reads, uses non-log transformed values for deciding cutoffs.

filter_vdj_chain_count(
  sce,
  tra_range = c(0, 2),
  trb_range = c(0, 1),
  igl_range = c(0, 2),
  igk_range = c(0, 2),
  igh_range = c(0, 1),
  tcr_and_bcr_allowed = TRUE,
  only_filter_if_any_vdj_hits = TRUE
)

Arguments

sce

SingleCellExperiment object
tcr_and_bcr_allowed

whether reads to both TRA/TRB locus and IGL/IGK/IGH locus are allowed on a single barcode - if FALSE, barcodes with reads to both will be removed
only_filter_if_any_vdj_hits

whether barcodes should only be filtered if there are any TRA/TRB/IGL/IGK/IGH reads at all - for diverse populations with non B/T cells, should be set to TRUE in order to avoid meaningless filtering on non B/T cells
min_tra

range of unique TRA sequences allowed per barcode. Barcodes with less than the first number and greater than the second number will be removed
min_trb

range of unique TRB sequences allowed per barcode. Barcodes with less than the first number and greater than the second number will be removed
min_igl

range of unique IGL sequences allowed per barcode. Barcodes with less than the first number and greater than the second number will be removed
min_igh

range of unique IGH sequences allowed per barcode. Barcodes with less than the first number and greater than the second number will be removed

Value

Boolean filter with TRUE for cells kept and FALSE for cells outside the allowed ranges.

Examples

NULL
#> NULL