tagClusterConvertors: Private functions to convert TC formats

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Interconvert tag clusters (TC) formats used in classes CAGEset (data.frame) and CAGEexp (GRanges).

Usage

TCgranges2dataframe(gr)

TCdataframe2granges(df)

Arguments

gr	Consensus clusters in GRanges format.
df	Consensus clusters in data.frame format.

Details

The original format used in CAGEset objects follows BED ("0-based") conventsion for the start and end coordinates. On the other hand, the GRanges objects used in CAGEexp objects follow the "1-based" convention. Therefore a value of 1 has to be added or subtracted to the start positions when converting between both formats.

See Also

Other df2granges converters: consensusClusterConvertors

Examples

df <- tagClusters(exampleCAGEset, 1)
head(df)
gr <- CAGEr:::TCdataframe2granges(df)
gr
head(CAGEr:::TCgranges2dataframe(gr))
# No exact round-trip because start and end were not integer in df.
identical(df, CAGEr:::TCgranges2dataframe(gr))
if (! all(df == CAGEr:::TCgranges2dataframe(gr)))
  stop("No round-trip between TCdataframe2granges and TCgranges2dataframe")

tagClustersGR(exampleCAGEexp)
head(CAGEr:::TCgranges2dataframe(CAGEr:::tagClustersGR(exampleCAGEexp, 1)))

CAGEr documentation built on Jan. 17, 2021, 2 a.m.