FunGeST / Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
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preprocessInput_snv throw errors using example data #1

Closed likelet closed 6 years ago

likelet commented 6 years ago

I am going to analyze my own data by using Palimpsest. Befored that, I tested the installation with following command. It returned errors that seems resulted from code?

my cmd

suppressMessages(library(Palimpsest))
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))
ref_genome <- BSgenome.Hsapiens.UCSC.hg19
#load ref data 
load("Palimpsest-master/data/ensgene_hg19.RData")
load("Palimpsest-master/data/cytoband_hg19.RData")
# load rawdata 
datadir <- "Palimpsest-master//RUNNING_PALIMPSEST_EXAMPLE/LiC1162"
#result DIR
resdir <- "Results";if(!file.exists(resdir)) dir.create(resdir)

#test
load(file.path(datadir,"mut_data.RData"))
load(file.path(datadir,"cna_data.RData"))
load(file.path(datadir,"annot_data.RData"))
load(file.path(datadir,"sv_data.RData"))

# Annotating the mutation data with necessary information
  vcf <- preprocessInput_snv(input_data = mut_data,
                              ensgene = ensgene,
                              reference_genome = ref_genome)

it throw errors

> vcf <- preprocessInput_snv(input_data = mut_data,
+                               ensgene = ensgene,
+                               reference_genome = ref_genome)
[1] "Annotating mutation data:"
  |================================================================================================================================================| 100%
Error in ensgene[match(vcf$Associated.Gene.Name, ensgene$Associated.Gene.Name),  : 
  non-numeric argument to binary operator

Any solutions ? my session info

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux

Matrix products: default
BLAS: /usr/lib/R/lib/libRblas.so
LAPACK: /usr/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.46.0                   rtracklayer_1.38.3                Biostrings_2.46.0                
 [5] XVector_0.18.0                    Palimpsest_1.0.0                  GenomicRanges_1.30.3              GenomeInfoDb_1.14.0              
 [9] IRanges_2.12.0                    S4Vectors_0.16.0                  BiocInstaller_1.28.0              NMF_0.21.0                       
[13] Biobase_2.38.0                    BiocGenerics_0.24.0               cluster_2.0.6                     rngtools_1.3.1                   
[17] pkgmaker_0.27                     registry_0.5                      RevoUtils_10.0.7                  RevoUtilsMath_10.0.1             

loaded via a namespace (and not attached):
 [1] httr_1.3.1                 RMySQL_0.10.15             bit64_0.9-7                foreach_1.4.5              gtools_3.5.0              
 [6] assertthat_0.2.0           blob_1.1.0                 GenomeInfoDbData_1.0.0     Rsamtools_1.30.0           yaml_2.1.16               
[11] progress_1.1.2             pillar_1.0.1               RSQLite_2.0                lattice_0.20-35            digest_0.6.15             
[16] RColorBrewer_1.1-2         colorspace_1.3-2           lsa_0.73.1                 Matrix_1.2-12              plyr_1.8.4                
[21] XML_3.98-1.11              bibtex_0.4.2               biomaRt_2.34.2             zlibbioc_1.24.0            xtable_1.8-2              
[26] RCircos_1.2.0              scales_0.5.0               gdata_2.18.0               BiocParallel_1.12.0        tibble_1.4.1              
[31] ggplot2_2.2.1              withr_2.1.2                SummarizedExperiment_1.8.1 GenomicFeatures_1.30.3     lazyeval_0.2.1            
[36] magrittr_1.5               memoise_1.1.0              SnowballC_0.5.1            doParallel_1.0.12          gplots_3.0.1              
[41] graph_1.56.0               tools_3.4.3                prettyunits_1.0.2          matrixStats_0.53.1         gridBase_0.4-7            
[46] stringr_1.3.1              munsell_0.4.3              plotrix_3.7                DelayedArray_0.4.1         AnnotationDbi_1.40.0      
[51] compiler_3.4.3             caTools_1.17.1             rlang_0.1.6                grid_3.4.3                 RCurl_1.95-4.10           
[56] iterators_1.0.9            VariantAnnotation_1.24.5   bitops_1.0-6               gtable_0.2.0               codetools_0.2-15          
[61] DBI_1.0.0                  reshape2_1.4.3             R6_2.2.2                   GenomicAlignments_1.14.2   bit_1.1-12                
[66] Rgraphviz_2.22.0           KernSmooth_2.23-15         stringi_1.2.2              Rcpp_0.12.14    
likelet commented 6 years ago

Well, it seems an accidental error, I reload the env and it's gone.