SigHotSpotter_pipeline: General Pipeline Call to SigHotSpotter

In saschajung/Intercom: Reconstruction of Functional Cell-Cell Communication Networks

General Pipeline Call to SigHotSpotter

Description

The function computes compatibility scores for signaling intermediates

Usage

SigHotSpotter_pipeline(
  species,
  idata,
  cutoff,
  DE_Genes,
  percentile,
  invert_DE = FALSE,
  showprogress = TRUE,
  ncores = 4
)

Arguments

species	Currently supported species: "HUMAN", "MOUSE"
idata	Data frame of input data. Rows correspond to genes, columns to cells
cutoff	Maximum number of zero-value genes, above this cutoff the genes are excluded
DE_Genes	(Differential) expression dataset as a one column data frame (1 for up-regulated, -1 for down-regulated genes)
percentile	Predicted intermediates are taken into account above this threshold
invert_DE	If the differential expression should be inverted (default: FALSE)
showprogress	shows progress bar in shiny app if set to TRUE, set it to FALSE in batch mode without GUI (default: TRUE)
ncores	Number of cores to use (default: 4)

Value

Compatibility scores

saschajung/Intercom documentation built on May 27, 2023, 5:11 p.m.