variantCounts: counts number of variants in certain affect categories use...
In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset
Description
Usage
Arguments
Value
Examples
Description
counts number of variants in certain affect categories
use with plyr::ldply() on VCFList objects to create a table.
Usage
1
variantCounts(data, unique = TRUE)
Arguments
data
tidyVCF with 'EFF' field parsed
unique
logical, if true only unique variants will be counted
Value
a single row dataframe with variant counts
Examples
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geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download and compile a list of VCF files
myVCFList <- VCFList(geneInfo)
## tabultate unique variants
plyr::ldply(myVCFList, variantCounts, unique=TRUE, .id="transcript_ID")
# tabulate total counts of variants relative to the reference sequence.
plyr::ldply(myVCFList, variantCounts, unique=TRUE, .id="transcript_ID")
wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.
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Description Usage Arguments Value Examples
Description
counts number of variants in certain affect categories use with plyr::ldply() on VCFList objects to create a table.
Usage
1 | variantCounts(data, unique = TRUE)
|
Arguments
data |
tidyVCF with 'EFF' field parsed |
unique |
logical, if true only unique variants will be counted |
Value
a single row dataframe with variant counts
Examples
1 2 3 4 5 6 7 8 9 10 | geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download and compile a list of VCF files
myVCFList <- VCFList(geneInfo)
## tabultate unique variants
plyr::ldply(myVCFList, variantCounts, unique=TRUE, .id="transcript_ID")
# tabulate total counts of variants relative to the reference sequence.
plyr::ldply(myVCFList, variantCounts, unique=TRUE, .id="transcript_ID")
|
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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