NoiseFiltering {DIscBIO}

Noise Filtering

Description

Given a matrix or data frame of count data, this function estimates the size factors as follows: Each column is divided by the geometric means of the rows. The median (or, if requested, another location estimator) of these ratios (skipping the genes with a # geometric mean of zero) is used as the size factor for this column. Source: DESeq package.

Usage

NoiseFiltering(
  object,
  percentile = 0.8,
  CV = 0.3,
  geneCol = "yellow",
  FgeneCol = "black",
  erccCol = "blue",
  Val = TRUE,
  plot = TRUE,
  export = FALSE,
  quiet = FALSE,
  filename = "Noise_filtering_genes_test"
)

## S4 method for signature 'DISCBIO'
NoiseFiltering(
  object,
  percentile = 0.8,
  CV = 0.3,
  geneCol = "yellow",
  FgeneCol = "black",
  erccCol = "blue",
  Val = TRUE,
  plot = TRUE,
  export = FALSE,
  quiet = FALSE,
  filename = "Noise_filtering_genes_test"
)

Arguments

object

DISCBIO class object.

percentile

A numeric value of the percentile. It is used to validate the ERCC spik-ins. Default is 0.8.

CV

A numeric value of the coefficient of variation. It is used to validate the ERCC spik-ins. Default is 0.5.

geneCol

Color of the genes that did not pass the filtration.

FgeneCol

Color of the genes that passt the filtration.

erccCol

Color of the ERCC spik-ins.

Val

A logical vector that allows plotting only the validated ERCC spike-ins. Default is TRUE. If Val=FALSE will plot all the ERCC spike-ins.

plot

A logical vector that allows plotting the technical noise. Default is TRUE.

export

A logical vector that allows writing the final gene list in excel file. Default is TRUE.

quiet

if 'TRUE', suppresses printed output

filename

Name of the exported file (if 'export=TRUE')

Value

The DISCBIO-class object input with the noiseF slot filled.

Note

This function should be used only if the dataset has ERCC.

Examples

sc <- DISCBIO(valuesG1msTest) # changes signature of data
sd_filtered <- NoiseFiltering(sc, export = FALSE)
str(sd_filtered)