CallSupport

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.