read.metharray.sheet Basename issue

[keeblee]

I have an issue for read.metharray.sheet. In Basename, c(" inserted. How can I remove it?

SampleSheet.csv is located in /disk2/kb/samples/EPICv1. idat files are located in /disk2/kb/samples/EPICv1/207179230070 and /disk2/kb/samples/EPICv1/207179230101.

My code and SeesionInfo are below.

Code `

basedir <- c('/disk2/kb/samples/EPICv1') targets <- read.metharray.sheet(basedir, pattern = "csv$", ignore.case = TRUE, recursive = TRUE, verbose = TRUE) [read.metharray.sheet] Found the following CSV files: [1] "/disk2/kb/samples/EPICv1/SampleSheet.csv" targets Sample_Name Sample_Well Sample_Plate Sample_Group Pool_ID person age sex 1 X0uM-1 GroupA NA NA NA 2 X0uM-2 GroupA NA NA NA 3 X1uM-1 GroupA NA NA NA 4 X1uM-2 GroupA NA NA NA 5 X0uM-3 GroupA NA NA NA 6 X0uM-4 GroupA NA NA NA 7 X3uM-1 GroupB NA NA NA 8 X3uM-2 GroupB NA NA NA 9 X3uM-3 GroupB NA NA NA 10 X3uM-4 GroupB NA NA NA status Array Slide 1 NA R01C01 207179230070 2 NA R02C01 207179230070 3 NA R03C01 207179230070 4 NA R04C01 207179230070 5 NA R05C01 207179230070 6 NA R06C01 207179230070 7 NA R01C01 207179230101 8 NA R02C01 207179230101 9 NA R05C01 207179230101 10 NA R06C01 207179230101 Basename 1 c("/disk2/kb/samples/EPICv1/207179230070/207179230070_R01C01 2 c("/disk2/kb/samples/EPICv1/207179230070/207179230070_R02C01 3 c("/disk2/kb/samples/EPICv1/207179230070/207179230070_R03C01 4 c("/disk2/kb/samples/EPICv1/207179230070/207179230070_R04C01 5 c("/disk2/kb/samples/EPICv1/207179230070/207179230070_R05C01 6 c("/disk2/kb/samples/EPICv1/207179230070/207179230070_R06C01 7 c("/disk2/kb/samples/EPICv1/207179230101/207179230101_R01C01 8 c("/disk2/kb/samples/EPICv1/207179230101/207179230101_R02C01 9 c("/disk2/kb/samples/EPICv1/207179230101/207179230101_R05C01 10 c("/disk2/kb/samples/EPICv1/207179230101/207179230101_R06C01`

` > sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] 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 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Asia/Seoul tzcode source: system (glibc) attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] minfi_1.46.0 bumphunter_1.42.0 [3] locfit_1.5-9.8 iterators_1.0.14 [5] foreach_1.5.2 Biostrings_2.68.1 [7] XVector_0.40.0 SummarizedExperiment_1.30.2 [9] Biobase_2.60.0 MatrixGenerics_1.12.2 [11] matrixStats_1.0.0 GenomicRanges_1.52.0 [13] GenomeInfoDb_1.36.1 IRanges_2.34.1 [15] S4Vectors_0.38.1 BiocGenerics_0.46.0 loaded via a namespace (and not attached): [1] beanplot_1.3.1 DBI_1.1.3 [3] bitops_1.0-7 biomaRt_2.56.1 [5] rlang_1.1.1 magrittr_2.0.3 [7] scrime_1.3.5 compiler_4.3.1 [9] RSQLite_2.3.1 GenomicFeatures_1.52.1 [11] DelayedMatrixStats_1.22.1 png_0.1-8 [13] vctrs_0.6.3 quadprog_1.5-8 [15] stringr_1.5.0 pkgconfig_2.0.3 [17] crayon_1.5.2 fastmap_1.1.1 [19] dbplyr_2.3.2 utf8_1.2.3 [21] Rsamtools_2.16.0 tzdb_0.4.0 [23] preprocessCore_1.62.1 purrr_1.0.1 [25] bit_4.0.5 zlibbioc_1.46.0 [27] cachem_1.0.8 progress_1.2.2 [29] blob_1.2.4 rhdf5filters_1.12.1 [31] DelayedArray_0.26.3 reshape_0.8.9 [33] Rhdf5lib_1.22.0 BiocParallel_1.34.2 [35] prettyunits_1.1.1 R6_2.5.1 [37] stringi_1.7.12 RColorBrewer_1.1-3 [39] genefilter_1.82.1 limma_3.56.2 [41] rtracklayer_1.60.0 Rcpp_1.0.10 [43] readr_2.1.4 illuminaio_0.42.0 [45] Matrix_1.5-4.1 splines_4.3.1 [47] tidyselect_1.2.0 yaml_2.3.7 [49] siggenes_1.74.0 codetools_0.2-19 [51] curl_5.0.1 doRNG_1.8.6 [53] lattice_0.21-8 tibble_3.2.1 [55] plyr_1.8.8 KEGGREST_1.40.0 [57] askpass_1.1 survival_3.5-5 [59] BiocFileCache_2.8.0 xml2_1.3.4 [61] mclust_6.0.0 pillar_1.9.0 [63] filelock_1.0.2 rngtools_1.5.2 [65] generics_0.1.3 RCurl_1.98-1.12 [67] hms_1.1.3 sparseMatrixStats_1.12.2 [69] xtable_1.8-4 glue_1.6.2 [71] tools_4.3.1 BiocIO_1.10.0 [73] data.table_1.14.8 annotate_1.78.0 [75] GenomicAlignments_1.36.0 GEOquery_2.68.0 [77] XML_3.99-0.14 rhdf5_2.44.0 [79] grid_4.3.1 tidyr_1.3.0 [81] AnnotationDbi_1.62.1 base64_2.0.1 [83] nlme_3.1-162 GenomeInfoDbData_1.2.10 [85] nor1mix_1.3-0 HDF5Array_1.28.1 [87] restfulr_0.0.15 cli_3.6.1 [89] rappdirs_0.3.3 fansi_1.0.4 [91] S4Arrays_1.0.4 dplyr_1.1.2 [93] digest_0.6.32 rjson_0.2.21 [95] memoise_2.0.1 multtest_2.56.0 [97] lifecycle_1.0.3 httr_1.4.6 [99] openssl_2.0.6 bit64_4.0.5 [101] MASS_7.3-60`