DBanalysis: Perform differential binding analysis

In TCseq: Time course sequencing data analysis

Description

This function performs differetial analysis by fitting read counts to a negative binomial generalized linear model.

Usage

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

Arguments

object	a TCA object.
categories	character string indicating levels of which factor (column in the design slot) are compared in the differential analysis. For time course analysis, the default factor is timepoint'.
norm.lib	logical indicating whether or not use effective library size when perform normalization. See 'Details' of counts
filter.type	character string indicating which type of count (raw or normalized) is used when doing filtering. Options are 'raw', cpm', 'rpkm', 'NULL'. NULL' means no filtering will be performed.
filter.value	A numberic value; if values of selected filter.type ('raw', cpm', 'rpkm') of a genomic feature are larger than the filter.value in at least a certain number (samplePassfilter) of samples/libraries for any of the conditions, such genomic feature will be kept; otherwise the genomic feature will be dropped.
samplePassfilter	numberic value indicating the least number of samples/libraries a genomic feature with counts (raw or normalized) more than filter.value for all conditions if such genomic feature will be kept.
...	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 glms 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)

TCseq documentation built on Nov. 8, 2020, 5:46 p.m.