DiffBind Error in if (file.info(peaks)$size > 0) { : missing value where TRUE/FALSE needed
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Entering edit mode
Alexandre • 0
@095e334e
Last seen 1 day ago
Hong Kong

Hi,

I am trying to read a DBA object from a Samplesheet but DiffBind throws me an error despite having the file paths correctly set.

library(DiffBind)
setwd("C:/Users/alexa/Documents/HKU/diffbind_data/")

samples <- read.csv(file = "diffbind_design.csv")
samples <- dba(sampleSheet = samples)

all files are under this directory C:/Users/alexa/Documents/HKU/diffbind_data/

enter image description here

csv file looks like that:

enter image description here



 sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] DiffBind_3.2.2              SummarizedExperiment_1.22.0
 [3] Biobase_2.52.0              MatrixGenerics_1.4.0       
 [5] matrixStats_0.59.0          GenomicRanges_1.44.0       
 [7] GenomeInfoDb_1.28.0         IRanges_2.26.0             
 [9] S4Vectors_0.30.0            BiocGenerics_0.38.0        

loaded via a namespace (and not attached):
  [1] backports_1.2.1          GOstats_2.58.0          
  [3] BiocFileCache_2.0.0      plyr_1.8.6              
  [5] GSEABase_1.54.0          splines_4.1.0           
  [7] BiocParallel_1.26.0      ggplot2_3.3.4           
  [9] amap_0.8-18              digest_0.6.27           
 [11] invgamma_1.1             GO.db_3.13.0            
 [13] SQUAREM_2021.1           fansi_0.5.0             
 [15] magrittr_2.0.1           checkmate_2.0.0         
 [17] memoise_2.0.0            BSgenome_1.60.0         
 [19] base64url_1.4            limma_3.48.0            
 [21] Biostrings_2.60.1        annotate_1.70.0         
 [23] systemPipeR_1.26.2       bdsmatrix_1.3-4         
 [25] prettyunits_1.1.1        jpeg_0.1-8.1            
 [27] colorspace_2.0-1         blob_1.2.1              
 [29] rappdirs_0.3.3           apeglm_1.14.0           
 [31] ggrepel_0.9.1            dplyr_1.0.6             
 [33] crayon_1.4.1             RCurl_1.98-1.3          
 [35] jsonlite_1.7.2           graph_1.70.0            
 [37] genefilter_1.74.0        brew_1.0-6              
 [39] survival_3.2-11          VariantAnnotation_1.38.0
 [41] glue_1.4.2               gtable_0.3.0            
 [43] zlibbioc_1.38.0          XVector_0.32.0          
 [45] DelayedArray_0.18.0      V8_3.4.2                
 [47] Rgraphviz_2.36.0         scales_1.1.1            
 [49] pheatmap_1.0.12          mvtnorm_1.1-2           
 [51] DBI_1.1.1                edgeR_3.34.0            
 [53] Rcpp_1.0.6               xtable_1.8-4            
 [55] progress_1.2.2           emdbook_1.3.12          
 [57] bit_4.0.4                rsvg_2.1.2              
 [59] AnnotationForge_1.34.0   truncnorm_1.0-8         
 [61] httr_1.4.2               gplots_3.1.1            
 [63] RColorBrewer_1.1-2       ellipsis_0.3.2          
 [65] pkgconfig_2.0.3          XML_3.99-0.6            
 [67] dbplyr_2.1.1             locfit_1.5-9.4          
 [69] utf8_1.2.1               tidyselect_1.1.1        
 [71] rlang_0.4.11             AnnotationDbi_1.54.1    
 [73] munsell_0.5.0            tools_4.1.0             
 [75] cachem_1.0.5             generics_0.1.0          
 [77] RSQLite_2.2.7            stringr_1.4.0           
 [79] fastmap_1.1.0            yaml_2.2.1              
 [81] bit64_4.0.5              caTools_1.18.2          
 [83] purrr_0.3.4              KEGGREST_1.32.0         
 [85] RBGL_1.68.0              xml2_1.3.2              
 [87] biomaRt_2.48.1           compiler_4.1.0          
 [89] rstudioapi_0.13          filelock_1.0.2          
 [91] curl_4.3.1               png_0.1-7               
 [93] tibble_3.1.2             stringi_1.6.1           
 [95] GenomicFeatures_1.44.0   lattice_0.20-44         
 [97] Matrix_1.3-3             vctrs_0.3.8             
 [99] pillar_1.6.1             lifecycle_1.0.0         
[101] irlba_2.3.3              data.table_1.14.0       
[103] bitops_1.0-7             rtracklayer_1.52.0      
[105] R6_2.5.0                 BiocIO_1.2.0            
[107] latticeExtra_0.6-29      hwriter_1.3.2           
[109] ShortRead_1.50.0         KernSmooth_2.23-20      
[111] MASS_7.3-54              gtools_3.9.2            
[113] assertthat_0.2.1         Category_2.58.0         
[115] rjson_0.2.20             withr_2.4.2             
[117] GenomicAlignments_1.28.0 batchtools_0.9.15       
[119] Rsamtools_2.8.0          GenomeInfoDbData_1.2.6  
[121] hms_1.1.0                grid_4.1.0              
[123] DOT_0.1                  coda_0.19-4             
[125] GreyListChIP_1.24.0      ashr_2.2-47             
[127] mixsqp_0.3-43            bbmle_1.0.23.1          
[129] numDeriv_2016.8-1.1      restfulr_0.0.13
DiffBind • 134 views
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2
Entering edit mode
Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

This is likely caused by your Peak files actually having an extension that is hidden by Windows. So instead of using sample1 in the Peaks column, use sample1.bed etc.

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