cds_coverage | R Documentation |
This function generates a data table that for each transcript contains at least i) its name; ii) its length or the length of its annotated coding sequence (if any); iii) the number of P-sites falling in its annotated coding sequence or in the whole transcript for all samples. When the coverage is computed for coding sequences and not whole transcripts, a chosen number of nucleotides at the beginning and/or at the end of the CDSs can be excluded for restricting the analysis to a portion of the original coding sequence. In this case the output data table includes an additional column reporting the length of the selected region. Moreover, either all P-sites or only in-frame P-sites can be considered. Finally, transcripts without annotated CDS are automatically discarded.
cds_coverage(
data,
annotation,
start_nts = 0,
stop_nts = 0,
in_frame = TRUE,
whole_transcript = FALSE
)
data |
Either list of data tables or GRangesList object from
|
annotation |
Data table as generated by |
start_nts |
Positive integer specifying the number of nucleotides at the
beginning of the coding sequences to be excluded from the analisys. Default
is 0. This parameter is considered only if |
stop_nts |
Positive integer specifying the number of nucleotides at the
end of the coding sequences to be excluded from the analisys. Default is 0.
This parameter is considered only if |
in_frame |
Logical value whether to consider only in-frame P-sites when
computing the coverage. Default is TRUE. This parameter is considered only
if |
whole_transcript |
Logical value whether to compute the coverage based on P-sites falling in any region of the transcript, i.e. CDS and UTRs. Default is FALSE. |
A data table.
## data(reads_list)
## data(mm81cdna)
##
## ## compute and add p-site datails
## psite_offset <- psite(reads_list, flanking = 6, extremity = "auto")
## reads_psite_list <- psite_info(reads_list, psite_offset)
##
## ## Compute the number of in-frame P-sites per whole coding sequences.
## psite_cds <- cds_coverage(reads_psite_list, mm81cdna)
##
## ## Compute the number of in-frame P-sites per coding sequences exluding
## ## the first 15 nucleotides and the last 10 nucleotides.
## psite_cds <- cds_coverage(reads_psite_list, mm81cdna,
## start_nts = 15, stop_nts = 10)
##
## ## Compute the number of P-sites per transcripts.
## psite_cds <- cds_coverage(reads_psite_list, mm81cdna,
## whole_transcript = TRUE)
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