filter_dds: Filter lowly abundant genes with the possibility of doing a...

In Ni-Ar/niar: Nice Interactive Analysis with R

Filter lowly abundant genes with the possibility of doing a normalisation on the genes to correct for trended biases. This function will not estimate size factors of a DESeq2 object, but it will add normalization factors to the DESeq2 object if the cyclic_loess is TRUE. Plotting options allow to see how the read distribution changes using different filtering and normalisation parameters

Description

Filter lowly abundant genes with the possibility of doing a normalisation on the genes to correct for trended biases. This function will not estimate size factors of a DESeq2 object, but it will add normalization factors to the DESeq2 object if the cyclic_loess is TRUE. Plotting options allow to see how the read distribution changes using different filtering and normalisation parameters

Usage

filter_dds(
  deseq_dataset,
  filt_method = c("sum", "mean", "max"),
  min_counts = 5,
  verbose = T,
  show_mltdnsty = T,
  cyclic_loess = F
)

Arguments

deseq_dataset
filt_method
min_counts
verbose
show_mltdnsty
cyclic_loess

Value

a DESeq2 object and a plot

Examples

dds_fltrd <- filter_dds(dds, filt_method = "mean")

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.