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Question: Error with mappability argument
0
gravatar for Ashley.Sawle
6 months ago by
Ashley.Sawle0 wrote:

I am getting an error when running chipenrich. It appears to be related to the new (as of v2.0.0) 'mappability' argument. The code I am running is:

> library(chipenrich)
> peaks <- read.delim("peakFile.test.bed")
> head(peaks)
  chrom     start       end
1  chr2  45979647  45980082
2 chr15  39960665  39961062
3 chr11 101312413 101312854
4  chrX  16637117  16637474
5  chr9  33221193  33221658
6  chr1  51787036  51787366
> results <- chipenrich(peaks, out_name = NULL, genome = "hg19", genesets = "GOBP", mappability = 50)
Error in file.exists(mappa_code) : invalid 'file' argument
> traceback()
3: file.exists(mappa_code)
2: setup_mappa(mappa_code = mappability, genome = genome, ldef_code = locusdef,
       ldef_obj = ldef)
1: chipenrich(peaks, out_name = NULL, genome = "hg19", genesets = "GOBP",
       mappability = 50)


If I provide the 'mappability' as a string it seems to work fine:

> results <- chipenrich(peaks, out_name = NULL, genome = "hg19", genesets = "GOBP", mappability = "50")
Reading peaks from data.frame...
Assigning peaks to genes with assign_peaks(...) ..
Mappability adjustment is enabled..
Test: ChIP-Enrich
Genesets: Gene Ontology Biological Process
Running tests..

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

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

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

other attached packages:
[1] magrittr_1.5     chipenrich_2.0.0 optparse_1.3.2  

loaded via a namespace (and not attached):
 [1] Biobase_2.36.2             org.Rn.eg.db_3.4.1         splines_3.4.0              Formula_1.2-1              stats4_3.4.0              
 [6] latticeExtra_0.6-28        GenomeInfoDbData_0.99.0    Rsamtools_1.28.0           RSQLite_1.1-2              backports_1.0.5           
[11] lattice_0.20-35            quantreg_5.33              digest_0.6.12              GenomicRanges_1.28.1       RColorBrewer_1.1-2        
[16] XVector_0.16.0             checkmate_1.8.2            sandwich_2.3-4             colorspace_1.3-2           rms_5.1-1                 
[21] htmltools_0.3.6            Matrix_1.2-10              plyr_1.8.4                 XML_3.98-1.7               SparseM_1.77              
[26] chipenrich.data_2.0.0      zlibbioc_1.22.0            org.Mm.eg.db_3.4.1         mvtnorm_1.0-6              scales_0.4.1              
[31] getopt_1.20.0              org.Dm.eg.db_3.4.1         MatrixModels_0.4-1         BiocParallel_1.10.1        htmlTable_1.9             
[36] tibble_1.3.0               mgcv_1.8-17                IRanges_2.10.0             ggplot2_2.2.1              TH.data_1.0-8             
[41] SummarizedExperiment_1.6.1 nnet_7.3-12                BiocGenerics_0.22.0        lazyeval_0.2.0             survival_2.41-3           
[46] polspline_1.1.12           memoise_1.1.0              MASS_7.3-47                nlme_3.1-131               foreign_0.8-68            
[51] tools_3.4.0                data.table_1.10.4          hms_0.3                    org.Hs.eg.db_3.4.1         multcomp_1.4-6            
[56] matrixStats_0.52.2         stringr_1.2.0              S4Vectors_0.14.0           munsell_0.4.3              cluster_2.0.6             
[61] DelayedArray_0.2.1         AnnotationDbi_1.38.0       Biostrings_2.44.0          compiler_3.4.0             GenomeInfoDb_1.12.0       
[66] grid_3.4.0                 RCurl_1.95-4.8             htmlwidgets_0.8            bitops_1.0-6               base64enc_0.1-3           
[71] codetools_0.2-15           gtable_0.2.0               DBI_0.6-1                  R6_2.2.0                   zoo_1.8-0                 
[76] GenomicAlignments_1.12.0   gridExtra_2.2.1            knitr_1.15.1               rtracklayer_1.36.0         Hmisc_4.0-3               
[81] readr_1.1.0                stringi_1.1.5              parallel_3.4.0             Rcpp_0.12.10               org.Dr.eg.db_3.4.1        
[86] rpart_4.1-11               acepack_1.4.1      

 

 

ADD COMMENTlink modified 6 months ago by rcavalca40 • written 6 months ago by Ashley.Sawle0
0
gravatar for rcavalca
6 months ago by
rcavalca40
United States
rcavalca40 wrote:

Hi Ashley,

Sorry for the delay in response, I was out of town. You're absolutely right. I should be coercing that parameter to a character before checking to see if it's a custom mappability file path that's given.

I've fixed this in the devel version, and will similarly fix it in the release version. It should show up in the Bioconductor build system in a day or so. For now, continue to pass the mappability as a string since that avoids the problem. Sorry for the trouble.

Thanks for using chipenrich,

Raymond

ADD COMMENTlink written 6 months ago by rcavalca40
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