ApplyMatrixByGroup: Apply function to integration sites per base per group

In wzthu/ATACFlow: An Easy-to-use Systematic pipeline for ATACseq data analysis

Apply function to integration sites per base per group

Description

Apply function to integration sites per base per group

Usage

ApplyMatrixByGroup(
  mat,
  groups,
  fun,
  normalize = TRUE,
  group.scale.factors = NULL,
  scale.factor = NULL
)

Arguments

mat	A cut matrix. See CutMatrix
groups	A vector of group identities, with the name of each element in the vector set to the cell name.
fun	Function to apply to each group of cells. For example, colSums or colMeans.
normalize	Perform sequencing depth and cell count normalization
group.scale.factors	Scaling factor for each group. Should be computed using the number of cells in the group and the average number of counts in the group.
scale.factor	Scaling factor to use. If NULL (default), will use the median normalization factor for all the groups.

Details

Perform colSums on a cut matrix with cells in the rows and position in the columns, for each group of cells separately.

Value

ApplyMatrixByGroup

wzthu/ATACFlow documentation built on Aug. 9, 2022, 2:24 a.m.