get_accessions: Obtain accession ids that carry a SNP. This function takes a...
In Gregor-Mendel-Institute/gwaR: A collection of R functions to conduct GWAS analysis (in Arabidopsis thaliana)
get_accessions R Documentation
Obtain accession ids that carry a SNP.
This function takes a table of gwas pvalues per chromosome and numeric position and retrieves the accessions that carry that SNP.
Description
Obtain accession ids that carry a SNP.
This function takes a table of gwas pvalues per chromosome and numeric position and retrieves the accessions that carry that SNP.
Usage
get_accessions(gwas_table, SNPrank, SNPmatrix = NULL)
Arguments
gwas_table
Object returned from format_gwas function
SNPrank
The (-log10(p)) rank of the SNP of interest
SNPmatrix
A path pointing to a SNPmatrix in .fst format.
Details
If no SNPmatrix is provided, the information will be obtained from 1001genomes.org
This function returns a single column named ACC_ID, that contains the accessions that contain the snp.
Gregor-Mendel-Institute/gwaR documentation built on Feb. 8, 2023, 8:34 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.
| get_accessions | R Documentation |
Obtain accession ids that carry a SNP. This function takes a table of gwas pvalues per chromosome and numeric position and retrieves the accessions that carry that SNP.
Description
Obtain accession ids that carry a SNP. This function takes a table of gwas pvalues per chromosome and numeric position and retrieves the accessions that carry that SNP.
Usage
get_accessions(gwas_table, SNPrank, SNPmatrix = NULL)
Arguments
gwas_table |
Object returned from |
SNPrank |
The (-log10(p)) rank of the SNP of interest |
SNPmatrix |
A path pointing to a SNPmatrix in .fst format. |
Details
If no SNPmatrix is provided, the information will be obtained from 1001genomes.org
This function returns a single column named ACC_ID, that contains the accessions that contain the snp.
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.