diversityStats: calculate nucleotide diversity statsistics for a...
In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset
Description
Usage
Arguments
Value
Examples
Description
calculate nucleotide diversity statsistics for a gene/transcript
use with plyr::ldply() on VCFList objects to create a table.
Usage
1
diversityStats(data, geneInfo = NULL)
Arguments
data
tidyVCF with 'EFF' field parsed and diversity calculated by position
geneInfo
Value
a row with nucleotide diversity statistics of the transcript.
Examples
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geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download and compile a list of VCF files
myVCFList <- VCFList(geneInfo)
## Parse EFF field
myVCFList <- plyr::llply(myVCFList, parseEFF)
## calculate site-wise nucleotide diversity
myVCFList <- plyr::llply(myVCFList, Nucleotide_diversity)
## tabulate diversity statistics
plyr::ldply(myVCFList, diversityStats, .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
calculate nucleotide diversity statsistics for a gene/transcript use with plyr::ldply() on VCFList objects to create a table.
Usage
1 | diversityStats(data, geneInfo = NULL)
|
Arguments
data |
tidyVCF with 'EFF' field parsed and diversity calculated by position |
geneInfo |
Value
a row with nucleotide diversity statistics of the transcript.
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 | geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download and compile a list of VCF files
myVCFList <- VCFList(geneInfo)
## Parse EFF field
myVCFList <- plyr::llply(myVCFList, parseEFF)
## calculate site-wise nucleotide diversity
myVCFList <- plyr::llply(myVCFList, Nucleotide_diversity)
## tabulate diversity statistics
plyr::ldply(myVCFList, diversityStats, .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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