read_assays_variants: Reading the assays of variants

In northNomad/tapestri.tools: A toolbox for the analysis of tapestri single cell multi-omics data

Reading the assays of variants

Description

read_assays_variants retrieves the assays of variants in an h5f.

Usage

read_assays_variants(
  h5f,
  included_assays = c("AF", "DP", "FILTER_MASK", "GQ", "NGT", "RGQ"),
  index_variants = NULL,
  index_cells = NULL,
  format = c("list", "RangedSummarizedExperiment")
)

Arguments

h5f	h5f
included_assays	A character vector. Selects which assays to retrieve. Possible values are AF variant allele frequencies (VAF) per cell and per variant DP read counts per cell and per variant FILTER_MASK binary value GQ genotype quality values per cell and per variant NGT genotypes per cell and per variant 0 = Reference (Wildtype) 1 = Heterozygous Mutant 2 = Homozygous Mutant 3 = Missing Data RGQ ???
index_variants	A named numeric vector. You should use get_variants_index to retrieve the indexes.
index_cells	A numeric vector. Specifies which cells (columns) to retrieve.
format	A character. Specifies the return format. Either a list or a RangedSummarizedExperiment.

Value

Default is a named list. Can return a RangedSummarizedExperiment if specified.

Examples

#' #Retrieving the NGT matrix for IDH1_R132H and NPM1c
## Not run: 
interesting_variants <- c(IDH1_R132H = "chr2:209113112:C/T", NPM1c = "chr5:170837543:C/CTCTG")
index <- get_variants_index(h5f, interesting_variants)
read_dna_variants(h5f, index_variants = index, included_assays = "NGT")

## End(Not run)

northNomad/tapestri.tools documentation built on May 31, 2024, 4:44 p.m.