preprocessing: preprocess the raw.data including quality control and...

In sqjin/scAI: integrative analysis of single-cell transcriptomic and epigenomic profiles

Description

preprocess the raw.data including quality control and normalization

Usage

preprocessing(object, assay = list("RNA", "ATAC"), minFeatures = 200,
  minCells = 3, minCounts = NULL, maxCounts = NULL,
  libararyflag = TRUE, logNormalize = TRUE)

Arguments

object	scAI object
assay	List of assay names to be normalized
minFeatures	Filter out cells with expressed features < minimum features
minCells	Filter out features expressing in less than minCells
minCounts	Filter out cells with expressed count < minCounts
maxCounts	Filter out cells with expressed count > minCounts
libararyflag	Whether do library size normalization
logNormalize	whether do log transformation

sqjin/scAI documentation built on Nov. 19, 2020, 4:04 p.m.