filter_vdj_chain_count: Get filter for barcodes based on the number of chains for...

In keshav-motwani/scanalysis: Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

Description

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

Usage

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

keshav-motwani/scanalysis documentation built on Feb. 4, 2021, 2:21 a.m.