RTCGA package | How to download methylation data to gain the same datasets as in RTCGA.methylation package? | Available cohorts | Downloading tarred files | Reading downloaded methylation dataset | Shortening paths and directories | Removing NA files from data2 | Paths to methylation data | Reading methylation data using readTCGA | Saving methylation data to RTCGA.methylation package
Package: RTCGA.methylation 1.40.0
Marcin Kosinski
RTCGA.methylation: Methylation datasets from The Cancer Genome Atlas Project
Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot.
Authors:
RTCGA.methylation_1.40.0.tar.gz
RTCGA.methylation_1.40.0.tar.gz(r-4.7-any)RTCGA.methylation_1.40.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RTCGA.methylation/json (API)
| # Install 'RTCGA.methylation' in R: |
| install.packages('RTCGA.methylation', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rtcga/rtcga/issues
Datasets:
- BRCA.methylation - Methylation datasets from TCGA project
- COAD.methylation - Methylation datasets from TCGA project
- COADREAD.methylation - Methylation datasets from TCGA project
- GBM.methylation - Methylation datasets from TCGA project
- GBMLGG.methylation - Methylation datasets from TCGA project
- KIPAN.methylation - Methylation datasets from TCGA project
- KIRC.methylation - Methylation datasets from TCGA project
- KIRP.methylation - Methylation datasets from TCGA project
- LAML.methylation - Methylation datasets from TCGA project
- LUAD.methylation - Methylation datasets from TCGA project
- LUSC.methylation - Methylation datasets from TCGA project
- OV.methylation1 - Methylation datasets from TCGA project
- OV.methylation2 - Methylation datasets from TCGA project
- READ.methylation - Methylation datasets from TCGA project
- STAD.methylation - Methylation datasets from TCGA project
- STES.methylation - Methylation datasets from TCGA project
- UCEC.methylation - Methylation datasets from TCGA project
On BioConductor:RTCGA.methylation-1.39.0(data/experiment 3.24)RTCGA.methylation-1.40.0(data/experiment 3.23)
Last updated from:dafcf06125 (on RELEASE_3_23). Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: no.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 157 | ||
| linux-devel | WARNING | 822 | ||
| source / vignettes | OK | 1107 | ||
| linux-release | WARNING | 981 |
Exports:
Dependencies:abindaskpassassertthatbackportsbase64encbitopsbootbroombslibcachemcarcarDataclicolorspacecommonmarkcorrplotcowplotcpp11curldata.tableDerivdigestdoBydplyrevaluateexactRankTestsfarverfastmapfontawesomeforecastFormulafracdifffsgenericsggplot2ggpubrggrepelggsciggsignifggtextggthemesgluegridExtragridtextgtablehighrhtmltoolshttrisobandjpegjquerylibjsonliteknitrlabelinglatticelifecyclelitedownlme4lmtestmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpngpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrlangrmarkdownrstatixRTCGArvestS7sassscalesselectrSparseMstringistringrsurvivalsurvminersystibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisviridisLitewithrxfunXMLxml2yamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Methylation datasets from TCGA project | BRCA.methylation BRCA.methylation,COAD.methylation,COADREAD.methylation,GBM.methylation,GBMLGG.methylation,KIPAN.methylation,KIRC.methylation,KIRP.methylation,LAML.methylation,LUAD.methylation,LUSC.methylation,OV.methylation,OV.methylation1,OV.methylation2,READ.methylation,STAD.methylation,STES.methylation,UCEC.methylation COAD.methylation COADREAD.methylation GBM.methylation GBMLGG.methylation KIPAN.methylation KIRC.methylation KIRP.methylation LAML.methylation LUAD.methylation LUSC.methylation methylation OV.methylation1 OV.methylation2 READ.methylation STAD.methylation STES.methylation UCEC.methylation |
