DBanalysis: Perform differential expression analysis

In MengjunWu/TCseq: Time course sequencing data analysis

Perform differential expression analysis

Description

This function is a wrapper for the glmFit in edgeR package.

Usage

DBanalysis(
  object,
  categories = "timepoint",
  norm.lib = TRUE,
  filter.type = NULL,
  filter.value = NULL,
  samplePassfilter = 2,
  ...
)

Arguments

object	a TCA object.
categories	character string giving which column in design will be used for differential analysis. For time course analysis, the default column is "timepoint".
norm.lib	logical indicating whether or not use effective library size when perform normalization. See counts for more details.
filter.type	character string indicating which type of count (raw or normalized) is used when performing filtering. Options are "raw", "cpm", "rpkm", "NULL". No filtering will be performed when using "NULL'.
filter.value	a numberic value; minimum values of selected filter.type ("raw", "cpm", "rpkm"). It is used in combination with samplePassfilter.
samplePassfilter	a numberic value indicating the minimum number of samples/libraries in which a genomic feature has counts value (raw or normalized) more than filter.value. Smaller than this number, the genomic feature will be filtered out.
...	additional arguments passed to glmFit from edgeR package.

Details

The differetial event is detected by using the generalized linear model (GLM) methods (McCarthy et al, 2012). This function fits the read counts of each genes to a negative binomial glm by using glmFit function from edgeR. To further test the significance of changes, see DBresult, TopDBresult

Value

A TCA object

Author(s)

Mengjun Wu, Lei Gu

References

McCarthy,D.J.,Chen, Y., & Smyth, G. K.(2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic acids research 40, 4288-4297.

See Also

DBresult, TopDBresult

Examples

data(tca_ATAC)
tca_ATAC <- DBanalysis(tca_ATAC)

MengjunWu/TCseq documentation built on May 15, 2023, 9:47 p.m.