query.maf.hg19 different numbers of column length

[yujung-c]

Objective Combine "Simple somatic mutation" in TCGA-LUAD

Code

# library -----------------------------------------------------------------
library(TCGAbiolinks)
library(MultiAssayExperiment)
library("Bioc2017.TCGAbiolinks.ELMER")
library(MultiAssayExperiment)
library(ELMER)
library(tidyr)
library(maftools)
library(dplyr)
library(tibble)
library(ComplexHeatmap)
library(SummarizedExperiment)
library(DT)
library(sesame)
library(UCSCXenaTools)
library(parallel)

# # Use GDCquery, GDCdownload and GDCpreprare to downoad MAF aligned --------

query.maf.hg19 <- GDCquery(project = "TCGA-LUAD", 
                           data.category = "Simple nucleotide variation", 
                           data.type = "Simple somatic mutation",
                           access = "open", 
                           legacy = TRUE)

GDCdownload(query.maf.hg19,method = "api",  files.per.chunk=10)

maf <- GDCprepare(query.maf.hg19)

Screenshot or illustration

packageVersion

packageVersion("TCGAbiolinks") [1] '2.22.4'

R version details

```R R.Version() $platform [1] "x86_64-redhat-linux-gnu" $arch [1] "x86_64" $os [1] "linux-gnu" $system [1] "x86_64, linux-gnu" $status [1] "" $major [1] "4" $minor [1] "1.3" $year [1] "2022" $month [1] "03" $day [1] "10" $`svn rev` [1] "81868" $language [1] "R" $version.string [1] "R version 4.1.3 (2022-03-10)" $nickname [1] "One Push-Up" ```

R session information

```R > sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Fedora Linux 35 (Workstation Edition) Matrix products: default BLAS/LAPACK: /usr/lib64/libflexiblas.so.3.1 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel grid stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] UCSCXenaTools_1.4.7 sesame_1.12.9 sesameData_1.12.0 [4] rmarkdown_2.14 ExperimentHub_2.2.1 AnnotationHub_3.2.2 [7] BiocFileCache_2.2.1 dbplyr_2.1.1 DT_0.22 [10] ComplexHeatmap_2.11.1 tibble_3.1.6 dplyr_1.0.8 [13] maftools_2.10.05 tidyr_1.2.0 ELMER_2.18.0 [16] ELMER.data_2.18.0 Bioc2017.TCGAbiolinks.ELMER_0.0.0.9000 MultiAssayExperiment_1.20.0 [19] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.1 [22] GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 [25] BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.62.0 [28] TCGAbiolinks_2.22.4 loaded via a namespace (and not attached): [1] rappdirs_0.3.3 rtracklayer_1.54.0 R.methodsS3_1.8.1 ggplot2_3.3.5 [5] bit64_4.0.5 knitr_1.38 DelayedArray_0.20.0 R.utils_2.11.0 [9] data.table_1.14.2 rpart_4.1.16 KEGGREST_1.34.0 RCurl_1.98-1.6 [13] AnnotationFilter_1.18.0 doParallel_1.0.17 generics_0.1.2 GenomicFeatures_1.46.5 [17] preprocessCore_1.56.0 RSQLite_2.2.12 proxy_0.4-26 bit_4.0.4 [21] tzdb_0.3.0 xml2_1.3.3 httpuv_1.6.5 assertthat_0.2.1 [25] xfun_0.30 hms_1.1.1 jquerylib_0.1.4 evaluate_0.15 [29] DNAcopy_1.68.0 promises_1.2.0.1 fansi_1.0.3 restfulr_0.0.13 [33] progress_1.2.2 DBI_1.1.2 htmlwidgets_1.5.4 reshape_0.8.9 [37] matlab_1.0.2 purrr_0.3.4 ellipsis_0.3.2 crosstalk_1.2.0 [41] ggpubr_0.4.0 backports_1.4.1 biomaRt_2.50.3 vctrs_0.4.1 [45] ensembldb_2.18.4 Cairo_1.5-15 abind_1.4-5 cachem_1.0.6 [49] withr_2.5.0 Gviz_1.38.4 BSgenome_1.62.0 checkmate_2.1.0 [53] vroom_1.5.7 GenomicAlignments_1.30.0 prettyunits_1.1.1 cluster_2.1.3 [57] DOSE_3.20.1 lazyeval_0.2.2 crayon_1.5.1 pkgconfig_2.0.3 [61] ProtGenerics_1.26.0 nnet_7.3-17 rlang_1.0.2 lifecycle_1.0.1 [65] downloader_0.4 filelock_1.0.2 dichromat_2.0-0 randomForest_4.7-1 [69] Matrix_1.4-1 carData_3.0-5 base64enc_0.1-3 GlobalOptions_0.1.2 [73] pheatmap_1.0.12 png_0.1-7 viridisLite_0.4.0 rjson_0.2.21 [77] bitops_1.0-7 R.oo_1.24.0 KernSmooth_2.23-20 Biostrings_2.62.0 [81] blob_1.2.3 shape_1.4.6 stringr_1.4.0 qvalue_2.26.0 [85] readr_2.1.2 jpeg_0.1-9 rstatix_0.7.0 ggsignif_0.6.3 [89] scales_1.2.0 memoise_2.0.1 magrittr_2.0.3 plyr_1.8.7 [93] zlibbioc_1.40.0 compiler_4.1.3 BiocIO_1.4.0 RColorBrewer_1.1-3 [97] clue_0.3-60 Rsamtools_2.10.0 cli_3.3.0 XVector_0.34.0 [101] patchwork_1.1.1 htmlTable_2.4.0 Formula_1.2-4 tidyselect_1.1.2 [105] stringi_1.7.6 TCGAbiolinksGUI.data_1.15.1 highr_0.9 yaml_2.3.5 [109] GOSemSim_2.20.0 latticeExtra_0.6-29 ggrepel_0.9.1 sass_0.4.1 [113] VariantAnnotation_1.40.0 fastmatch_1.1-3 tools_4.1.3 circlize_0.4.14 [117] rstudioapi_0.13 foreach_1.5.2 foreign_0.8-82 gridExtra_2.3 [121] ComplexUpset_1.3.3 digest_0.6.29 BiocManager_1.30.17 shiny_1.7.1.9003 [125] wheatmap_0.2.0 Rcpp_1.0.8.3 car_3.0-12 broom_0.8.0 [129] BiocVersion_3.14.0 later_1.3.0 httr_1.4.2 AnnotationDbi_1.56.2 [133] biovizBase_1.42.0 colorspace_2.0-3 rvest_1.0.2 XML_3.99-0.9 [137] splines_4.1.3 plotly_4.10.0 xtable_1.8-4 jsonlite_1.8.0 [141] R6_2.5.1 Hmisc_4.7-0 pillar_1.7.0 htmltools_0.5.2 [145] mime_0.12 glue_1.6.2 fastmap_1.1.0 BiocParallel_1.28.3 [149] class_7.3-20 interactiveDisplayBase_1.32.0 codetools_0.2-18 fgsea_1.20.0 [153] utf8_1.2.2 lattice_0.20-45 bslib_0.3.1 curl_4.3.2 [157] zip_2.2.0 GO.db_3.14.0 openxlsx_4.2.5 survival_3.3-1 [161] munsell_0.5.0 e1071_1.7-9 DO.db_2.9 GetoptLong_1.0.5 [165] GenomeInfoDbData_1.2.7 iterators_1.0.14 reshape2_1.4.4 gtable_0.3.0 ```