occurrences: Find the occurrences of each of a character vector of...
In Santaris/seqtools: Tools for oligonucleotide-centric sequence analysis
Description
Usage
Arguments
Value
Description
This function is used by TargetSurveyor
This function wraps Biostring functions to find the occurrence of targets sites in a sequence database
Usage
1
2
occurrences(target.sites, seqdb, seqdb.name = "unnamed_seqdb",
summarize = TRUE, no.mismatch = 0, ...)
Arguments
target.sites
a character vector of target sites, e.g. from the appropriate column of a target survey
seqdb
a DNAStringSet. If ensembl=TRUE, the sequence names needs to be formatted in a special way for the summarize function to work
seqdb.name
a character string to be used for generating column headers in the output
summarize
if TRUE (default) the results are processed to count the unique transcripts, genes and symbols that are hit
the
exact number of mismatches in each occurrence (defaults to 0)
Value
a data.frame with the same number of rows and ordering as target.sites
Santaris/seqtools documentation built on May 9, 2019, 12:44 p.m.
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Description Usage Arguments Value
Description
This function is used by TargetSurveyor This function wraps Biostring functions to find the occurrence of targets sites in a sequence database
Usage
1 2 | occurrences(target.sites, seqdb, seqdb.name = "unnamed_seqdb",
summarize = TRUE, no.mismatch = 0, ...)
|
Arguments
target.sites |
a character vector of target sites, e.g. from the appropriate column of a target survey |
seqdb |
a DNAStringSet. If ensembl=TRUE, the sequence names needs to be formatted in a special way for the summarize function to work |
seqdb.name |
a character string to be used for generating column headers in the output |
summarize |
if TRUE (default) the results are processed to count the unique transcripts, genes and symbols that are hit |
the |
exact number of mismatches in each occurrence (defaults to 0) |
Value
a data.frame with the same number of rows and ordering as target.sites
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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