countDNAPattern: Count the number of DNA pattern for each transcript, and...
In utr.annotation: Annotate Variants in the Untranslated Regions
Description
Usage
Arguments
Value
Description
countDNAPattern count the number of DNA pattern for each transcript, and concatenate the numbers with ";"
Usage
1
countDNAPattern(variantsTable, seqTable, dnaPattern, transcriptIdCol)
Arguments
variantsTable
variants table
seqTable
sequences table containing two columns: ensembl_transcript_id and seq. seq is the sequence of the variantType region: e.g. 5' UTR sequence or 3' UTR sequence. The seqTable is output from function getSeqTable.
dnaPattern
the string pattern that you want to count, for example "ATG"
transcriptIdCol
the ensemble transcript id column
Value
a list containing values for number of DNA pattern. Can be used to add new column to the variants table.
utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.
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Description Usage Arguments Value
Description
countDNAPattern count the number of DNA pattern for each transcript, and concatenate the numbers with ";"
Usage
1 | countDNAPattern(variantsTable, seqTable, dnaPattern, transcriptIdCol)
|
Arguments
variantsTable |
variants table |
seqTable |
sequences table containing two columns: ensembl_transcript_id and seq. seq is the sequence of the variantType region: e.g. 5' UTR sequence or 3' UTR sequence. The seqTable is output from function getSeqTable. |
dnaPattern |
the string pattern that you want to count, for example "ATG" |
transcriptIdCol |
the ensemble transcript id column |
Value
a list containing values for number of DNA pattern. Can be used to add new column to the variants table.
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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