filterdata {RaceID}

Data filtering

Description

This function allows filtering of genes and cells to be used in the RaceID3 analysis. It also can perform batch effect correction using an internal method or a recently published alternative mnnCorrect from the batchelor package.

Usage

filterdata(
  object,
  mintotal = 3000,
  minexpr = 5,
  minnumber = 5,
  LBatch = NULL,
  knn = 10,
  CGenes = NULL,
  FGenes = NULL,
  ccor = 0.4,
  bmode = "RaceID",
  verbose = TRUE
)

Arguments

object

SCseq class object.

mintotal

minimum total transcript number required. Cells with less than mintotal transcripts are filtered out. Default is 3000.

minexpr

minimum required transcript count of a gene in at least minnumber cells. All other genes are filtered out. Default is 5.

minnumber

See minexpr. Default is 5.

LBatch

List of experimental batches used for batch effect correction. Each list element contains a vector with cell names (i.e. column names of the input expression data) falling into this batch. Default is NULL, i.e. no batch correction.

knn

Number of nearest neighbors used to infer corresponding cell types in different batches. Defult is 10.

CGenes

List of gene names. All genes with correlated expression to any of the genes in CGenes are filtered out for cell type inference. Default is NULL.

FGenes

List of gene names to be filtered out for cell type inference. Default is NULL.

ccor

Correlation coefficient used as a trehshold for determining genes correlated to genes in CGenes. Only genes correlating less than ccor to all genes in CGenes are retained for analysis. Default is 0.4.

bmode

Method used for batch effect correction. Any of "RaceID","mnnCorrect". If mnnCorrect from the batchelor package is desired, this package needs to be installed from bioconductor. Default is "RaceID".

verbose

logical. If FALSE then status output messages are disabled. Default is TRUE.

Value

An SCseq class object with filtered and normalized expression data.

Examples

sc <- SCseq(intestinalDataSmall)
sc <- filterdata(sc)