addCDS: Add CDS to rowRanges of a transcript-level...
In mikelove/tximeta: Transcript Quantification Import with Automatic Metadata
addCDS R Documentation
Add CDS to rowRanges of a transcript-level SummarizedExperiment
Description
Working similarly to addExons, this function
can be used to add information about CDS (coding sequence)
to the SummarizedExperiment object. As not all transcripts
are coding, we have CDS information for only a subset of the
rows of the object. For this reason, a logical indicator for
whether the transcript is coding, mcols(se)$coding,
is added as a column to the metadata columns of the rowRanges
of the object. An additional column, mcols(se)$cds,
is added to the metadata columns, which is a GRangesList
with either the CDS regions (if the transcript is coding),
or the original transcript/exon ranges (if the transcript is non-coding).
This is necessary, as GRangesList cannot have NA elements.
As with addExons, this function is designed only
for transcript-level objects.
Usage
addCDS(se)
Arguments
se
the SummarizedExperiment
Value
a SummarizedExperiment
mikelove/tximeta documentation built on Feb. 26, 2024, 4:32 a.m.
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| addCDS | R Documentation |
Add CDS to rowRanges of a transcript-level SummarizedExperiment
Description
Working similarly to addExons, this function
can be used to add information about CDS (coding sequence)
to the SummarizedExperiment object. As not all transcripts
are coding, we have CDS information for only a subset of the
rows of the object. For this reason, a logical indicator for
whether the transcript is coding, mcols(se)$coding,
is added as a column to the metadata columns of the rowRanges
of the object. An additional column, mcols(se)$cds,
is added to the metadata columns, which is a GRangesList
with either the CDS regions (if the transcript is coding),
or the original transcript/exon ranges (if the transcript is non-coding).
This is necessary, as GRangesList cannot have NA elements.
As with addExons, this function is designed only
for transcript-level objects.
Usage
addCDS(se)
Arguments
se |
the SummarizedExperiment |
Value
a SummarizedExperiment
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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