PoisonAlien
commented
1 year ago Hi,
Sorry for the late reply. You don't need to use the extdata as in the vignette. It's only used there to access the example files bundled with the package. You can just specify the full path to your GISTIC files.
HCC.gistic = readGistic(gisticAllLesionsFile = "513001/all_lesions.conf_90.txt", ...)I hope this helps.
Describe the issue I created the GISTIC file from Gene Pattern website and downloaded it to my computer (It was the TCGA data for liver cancer). However, when I run the code I get an error report. I don't know what I am missing here. I would appreciate your help. Also, I wanted to know what "extdata" really specify?
Command all. Lesions <- system.file("extdata", "all_lesions.conf_90.txt", package = "maftools") amp.genes <- system.file("extdata", "amp_genes.conf_90.txt", package = "maftools") del.genes <- system.file("extdata", "del_genes.conf_90.txt", package = "maftools") scores.gis <- system.file("extdata", "scores.gistic", package = "maftools")
HCC.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, gisticDelGenesFile = del.genes, gisticScoresFile = scores.gis, isTCGA = TRUE)
Error: -Processing Gistic files.. Error in data.table::fread(input = gisticAllLesionsFile, stringsAsFactors = FALSE, : Input is empty or only contains BOM or terminal control characters
Session info
Matrix products: default
locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] mutSignatures_2.1.5 foreach_1.5.2 kableExtra_1.3.4
[4] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[7] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[10] tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
[13] pheatmap_1.0.12 NMF_0.26 Biobase_2.58.0
[16] cluster_2.1.4 rngtools_1.5.2 registry_0.5-1
[19] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.66.3 rtracklayer_1.58.0
[22] Biostrings_2.66.0 XVector_0.38.0 GenomicRanges_1.50.2
[25] GenomeInfoDb_1.34.9 IRanges_2.32.0 S4Vectors_0.36.2
[28] BiocGenerics_0.44.0 R.utils_2.12.2 R.oo_1.25.0
[31] R.methodsS3_1.8.2 tidyr_1.3.0 data.table_1.14.8
[34] maftools_2.14.0
loaded via a namespace (and not attached): [1] bitops_1.0-7 matrixStats_1.0.0 webshot_0.5.4 httr_1.4.6
[5] doParallel_1.0.17 RColorBrewer_1.1-3 tools_4.2.2 utf8_1.2.3
[9] R6_2.5.1 colorspace_2.1-0 DNAcopy_1.72.3 withr_2.5.0
[13] tidyselect_1.2.0 compiler_4.2.2 rvest_1.0.3 cli_3.6.1
[17] xml2_1.3.4 DelayedArray_0.24.0 scales_1.2.1 proxy_0.4-27
[21] systemfonts_1.0.4 digest_0.6.31 Rsamtools_2.14.0 svglite_2.1.1
[25] rmarkdown_2.22 pkgconfig_2.0.3 htmltools_0.5.5 MatrixGenerics_1.10.0
[29] fastmap_1.1.1 rlang_1.1.0 rstudioapi_0.14 BiocIO_1.8.0
[33] generics_0.1.3 BiocParallel_1.32.6 RCurl_1.98-1.12 magrittr_2.0.3
[37] GenomeInfoDbData_1.2.9 Matrix_1.5-3 Rcpp_1.0.10 munsell_0.5.0
[41] fansi_1.0.4 lifecycle_1.0.3 stringi_1.7.12 yaml_2.3.7
[45] SummarizedExperiment_1.28.0 zlibbioc_1.44.0 plyr_1.8.8 grid_4.2.2
[49] parallel_4.2.2 crayon_1.5.2 lattice_0.20-45 splines_4.2.2
[53] hms_1.1.3 knitr_1.43 pillar_1.9.0 rjson_0.2.21
[57] reshape2_1.4.4 codetools_0.2-19 XML_3.99-0.14 glue_1.6.2
[61] evaluate_0.21 BiocManager_1.30.20 vctrs_0.6.1 tzdb_0.4.0
[65] gtable_0.3.3 xfun_0.39 gridBase_0.4-7 restfulr_0.0.15
[69] pracma_2.4.2 viridisLite_0.4.2 survival_3.5-5 iterators_1.0.14
[73] GenomicAlignments_1.34.1 timechange_0.2.0
513001.zip