makeDistFeatureSampleTable: Summarises feature expression along specified factor and...

In iaaka/visutils: QC, analyse and visualize visium

Summarises feature expression along specified factor and sample

Description

summary statistics will be calculated for each dist-sample-feature combination

Usage

makeDistFeatureSampleTable(
  dist,
  sample,
  data,
  filter = NULL,
  FUN = mean,
  min.spots = 5,
  ncores = 1,
  per.spot.norm = TRUE
)

Arguments

dist	factor to summarise data along. Normally it is binnarised distance to something.
sample	character vector specifying sample
data	numeric matrix (probably sparse) with data to be summarised.
filter	spot filter, the variable to be used to subset spots (will be applied to dist, sample, and data). No filtering applied if NULL (default)
FUN	function to summarise the data (mean by default)
min.spots	minimal namber of spots for statistics to be calculated (5 by default)
ncores	number of cores to be used
per.spot.norm	whether to perform per-spot normalization (makes sence for celltype abundancies)

Value

3d (distance/feature/sample) numeric matrix with summarized data

iaaka/visutils documentation built on Jan. 17, 2025, 11:29 p.m.