Rationale
Package: vcf2mafR 0.0.0.9000
Sam El-Kamand
vcf2mafR: What the Package Does (One Line, Title Case)
What the package does (one paragraph).
Authors:
vcf2mafR_0.0.0.9000.tar.gz
vcf2mafR_0.0.0.9000.zip(r-4.7)vcf2mafR_0.0.0.9000.zip(r-4.6)vcf2mafR_0.0.0.9000.zip(r-4.5)
vcf2mafR_0.0.0.9000.tgz(r-4.6-any)vcf2mafR_0.0.0.9000.tgz(r-4.5-any)
vcf2mafR_0.0.0.9000.tar.gz(r-4.7-any)vcf2mafR_0.0.0.9000.tar.gz(r-4.6-any)
vcf2mafR_0.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
vcf2mafR/json (API)
| # Install 'vcf2mafR' in R: |
| install.packages('vcf2mafR', repos = c('https://ccicb.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/selkamand/vcf2mafr/issues
Last updated from:5be8185d17. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 134 | ||
| source / vignettes | OK | 203 | ||
| linux-release-x86_64 | OK | 126 | ||
| macos-release-arm64 | OK | 126 | ||
| macos-oldrel-arm64 | OK | 79 | ||
| windows-devel | OK | 93 | ||
| windows-release | OK | 86 | ||
| windows-oldrel | OK | 88 | ||
| wasm-release | OK | 133 |
Exports:df2mafpaths_to_sample_namesvalid_maf_columnsvcf2dfvcf2mafvcfs2mafvep_rank_biotypesvep_rank_consequences
Dependencies:apeassertionscliclusterdata.tabledigestdplyrgenericsgluelatticelifecyclemagrittrMASSMatrixmemusemgcvmutationtypesnlmepermutepillarpinfsc50pkgconfigR6Rcpprlangstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert cDNA_position to numeric indication of transcript length | cdna_to_transcript_length |
| Convert VCF-like data.frame to MAF | df2maf |
| Extract Sample Names From VCF filepath | paths_to_sample_names |
| Maf Column Names | valid_maf_columns |
| Convert a vepped VCF into a table ready to be passed into df2maf | vcf2df |
| Convert Annotated VCF to MAF-compatible data.frame | vcf2maf |
| Convert several VCF files into a cohort-level MAF | vcfs2maf |
| Rank VEP biotypes | vep_rank_biotypes |
| Rank VEP consequences | vep_rank_consequences |
