CallSupport: CallSupport
In CostaLab/sigurd: Single cell Genotyping Using RNA Data

CallSupport

R Documentation

CallSupport

Description

Check if a cell is supported by a set of variants.

Usage

CallSupport(
  SE,
  VOI_group1,
  VOI_group2,
  group1_name = "group1",
  group2_name = "group2",
  min_mutated_reads = 3,
  min_reads = 30,
  group_factor = NULL,
  verbose = TRUE,
  return_nonsupport = FALSE
)

Arguments

`SE`	SummarizedExperiment object.
`VOI_group1`	The variants supporting the first group.
`VOI_group2`	The variants supporting the second group.
`group1_name`	The name used for the first group.
`group2_name`	The name used for the second group.
`min_mutated_reads`	The minimum number of mutated reads in a cell supporting a group.
`min_reads`	Minimum number of reads per cell for a classification.
`group_factor`	How much higher has the mean allele frequency to be in group 1 when compared to group 2 and vice versa? Can be a vector of length 2.
`verbose`	Should the function be verbose? Default = TRUE
`return_nonsupport`	Should nonsupporting cells be return too? Default FALSE.
`group_of_interest`	The column data that divides the cells.