readIMGT: 'readIMGT' read in IMGT database
In dowser: B Cell Receptor Phylogenetics Toolkit
readIMGT R Documentation
readIMGT read in IMGT database
Description
Loads all reference germlines from an Immcantation-formatted IMGT database.
Usage
readIMGT(dir, quiet = FALSE)
Arguments
dir
directory containing Immcantation-formatted IMGT database
quiet
print warnings?
Details
Input directory must be formatted to Immcantation standard.
See https://changeo.readthedocs.io/en/stable/examples/igblast.html for example
of how to download.
Value
List of lists, leading to IMGT-gapped nucleotide sequences.
Structure of object is list[[locus]][[segment]]
locus refers to locus (e.g. IGH, IGK, TRA)
segment refers to gene segment caegory (V, D, or J)
Examples
# vdj_dir contains a minimal example of reference germlines
# (IGHV3-11*05, IGHD3-10*01 and IGHJ5*02)
# which are the gene assignments for ExamapleDb[1,]
vdj_dir <- system.file("extdata", "germlines", "imgt", "human", "vdj", package="dowser")
imgt <- readIMGT(vdj_dir)
dowser documentation built on May 29, 2024, 3:06 a.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.
| readIMGT | R Documentation |
readIMGT read in IMGT database
Description
Loads all reference germlines from an Immcantation-formatted IMGT database.
Usage
readIMGT(dir, quiet = FALSE)
Arguments
dir |
directory containing Immcantation-formatted IMGT database |
quiet |
print warnings? |
Details
Input directory must be formatted to Immcantation standard. See https://changeo.readthedocs.io/en/stable/examples/igblast.html for example of how to download.
Value
List of lists, leading to IMGT-gapped nucleotide sequences. Structure of object is list[[locus]][[segment]] locus refers to locus (e.g. IGH, IGK, TRA) segment refers to gene segment caegory (V, D, or J)
Examples
# vdj_dir contains a minimal example of reference germlines
# (IGHV3-11*05, IGHD3-10*01 and IGHJ5*02)
# which are the gene assignments for ExamapleDb[1,]
vdj_dir <- system.file("extdata", "germlines", "imgt", "human", "vdj", package="dowser")
imgt <- readIMGT(vdj_dir)
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.