tagClusterConvertors {CAGEr} | R Documentation |
Interconvert tag clusters (TC) formats used in classes CAGEset
(data.frame
) and CAGEexp (GRanges
).
TCgranges2dataframe(gr) TCdataframe2granges(df)
gr |
Consensus clusters in |
df |
Consensus clusters in |
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.
Other df2granges converters: consensusClusterConvertors
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)))