getCodingDiv: produce dataframe of unique variants on the coding sequence
In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset
Description
Usage
Arguments
Value
Examples
Description
produce dataframe of unique variants on the coding sequence
Usage
1
Arguments
data
tidyVCF with 'EFF' field parsed and 'Diversity' field calculated
Value
a dataframe of unique variants on the coding sequence
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download a single VCF
myVCF <- VCFByTranscript(geneInfo[1, ])
## Parse the EFF field of a single VCF:
myVCF <- parseEFF(myVCF)
## calculate site-wise nucleotide diversity of a single VCF
myVCF <- Nucleotide_diversity(myVCF)
# get unique coding variants with diversity
myCodingVariants <- getCodingDiv(myVCF)
## plot diversity of coding variants
plotCodingDiv(myCodingVariants)
wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.
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.
Description Usage Arguments Value Examples
Description
produce dataframe of unique variants on the coding sequence
Usage
1 |
Arguments
data |
tidyVCF with 'EFF' field parsed and 'Diversity' field calculated |
Value
a dataframe of unique variants on the coding sequence
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download a single VCF
myVCF <- VCFByTranscript(geneInfo[1, ])
## Parse the EFF field of a single VCF:
myVCF <- parseEFF(myVCF)
## calculate site-wise nucleotide diversity of a single VCF
myVCF <- Nucleotide_diversity(myVCF)
# get unique coding variants with diversity
myCodingVariants <- getCodingDiv(myVCF)
## plot diversity of coding variants
plotCodingDiv(myCodingVariants)
|
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.