Normalizedata: Normalizing and filtering

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

Normalizing and filtering

Description

This function allows filtering of genes and cells to be used in the downstream analysis.

Usage

Normalizedata(
  object,
  mintotal = 1000,
  minexpr = 0,
  minnumber = 0,
  maxexpr = Inf,
  downsample = FALSE,
  dsn = 1,
  rseed = NULL
)

## S4 method for signature 'DISCBIO'
Normalizedata(
  object,
  mintotal = 1000,
  minexpr = 0,
  minnumber = 0,
  maxexpr = Inf,
  downsample = FALSE,
  dsn = 1,
  rseed = NULL
)

Arguments

object	DISCBIO class object.
mintotal	minimum total transcript number required. Cells with less than mintotal transcripts are filtered out. Default is 1000.
minexpr	minimum required transcript count of a gene in at least minnumber cells. All other genes are filtered out. Default is 0.
minnumber	minimum number of cells that are expressing each gene at minexpr transcripts. Default is 0.
maxexpr	maximum allowed transcript count of a gene in at least a single cell after normalization or downsampling. All other genes are filtered out. Default is Inf.
downsample	A logical vector. Default is FALSE. If downsample is set to TRUE, then transcript counts are downsampled to mintotal transcripts per cell, instead of the normalization. Downsampled versions of the transcript count data are averaged across dsn samples
dsn	A numeric value of the number of samples to be used to average the downsampled versions of the transcript count data. Default is 1 which means that sampling noise should be comparable across cells. For high numbers of dsn the data will become similar to the median normalization.
rseed	Random integer to enforce reproducible clustering. results

Value

The DISCBIO-class object input with the ndata and fdata slots filled.

Examples

sc <- DISCBIO(valuesG1msTest) # changes signature of data

# In this case this function is used to normalize the reads
sc_normal <- Normalizedata(
  sc,
  mintotal = 1000, minexpr = 0, minnumber = 0, maxexpr = Inf,
  downsample = FALSE, dsn = 1, rseed = 17000
)
summary(sc_normal@fdata)

DIscBIO documentation built on Nov. 6, 2023, 5:08 p.m.