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View Code? Open in Web Editor NEWIdentification of candidate causal perturbations from differential gene expression data
Home Page: https://nuno-agostinho.github.io/cTRAP
License: Other
Identification of candidate causal perturbations from differential gene expression data
Home Page: https://nuno-agostinho.github.io/cTRAP
License: Other
Hi Nuno,
I've encountered some issues with the cTRAP WebApp and the R package. Here are the details:
The WebApp version of cTRAP, hosted here, is not working properly. After uploading Differentially Expression Data and loading cMAP Perturbations, attempting to perform an analysis by clicking on "Rank by similarity" results in the site getting a grey filter and loading indefinitely:
After following the R tutorial for the cTRAP R package, the plotTargetingDrugsVSsimilarPerturbations
function is not working as intended:
plotTargetingDrugsVSsimilarPerturbations(predicted, compareCompounds, column="spearman_rank")
#Resulting on the following error
> Columns 'broad id' and 'pubchem_cid' were matched based on 0 common values; to manually select columns to compare, please set arguments starting with 'keyCol'
I encounter both these errors when using the default Differentially Expression Data (diffExprStat) from the R package.
Thank you for your attention and your help!
Best regards,
Alex
Do you have a vignette tutorial code on how to use cTRAP on Seurat or scRNA-seq data please? Thank you!
Hi,
for some reason, when I am running the same code from this pdf, when I execute the line:
compareSmallMolecule$spearman <- compareAgainstL1000( diffExprStat, l1000perturbationsSmallMolecules, cellLine, method="spearman")
I am getting the following error:
Error in
.rowNamesDF<-
(x, value = value) : duplicate 'row.names' are not allowed
What might be the problem?
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_0.7.8 cTRAP_1.0.2 biomaRt_2.38.0 Biobase_2.42.0 BiocGenerics_0.28.0 DeMAND_1.12.0
[7] KernSmooth_2.23-15 limma_3.38.2
loaded via a namespace (and not attached):
[1] httr_1.3.1 jsonlite_1.5 bit64_0.9-7 R.utils_2.7.0 gtools_3.8.1
[6] assertthat_0.2.0 stats4_3.5.1 blob_1.1.1 yaml_2.2.0 progress_1.2.0
[11] slam_0.1-43 pillar_1.3.0 RSQLite_2.1.1 lattice_0.20-35 glue_1.3.0
[16] digest_0.6.18 colorspace_1.3-2 cowplot_0.9.3 Matrix_1.2-14 R.oo_1.22.0
[21] plyr_1.8.4 XML_3.98-1.16 pkgconfig_2.0.2 purrr_0.2.5 relations_0.6-8
[26] scales_1.0.0 gdata_2.18.0 BiocParallel_1.16.0 tibble_1.4.2 IRanges_2.16.0
[31] ggplot2_3.1.0 pbapply_1.3-4 lazyeval_0.2.1 magrittr_1.5 crayon_1.3.4
[36] memoise_1.1.0 R.methodsS3_1.7.1 gplots_3.0.1 tools_3.5.1 data.table_1.11.8
[41] prettyunits_1.0.2 hms_0.4.2 stringr_1.3.1 Rhdf5lib_1.4.0 S4Vectors_0.20.1
[46] munsell_0.5.0 cluster_2.0.7-1 AnnotationDbi_1.44.0 bindrcpp_0.2.2 compiler_3.5.1
[51] caTools_1.17.1.1 rlang_0.3.0.1 rhdf5_2.26.0 grid_3.5.1 RCurl_1.95-4.11
[56] marray_1.60.0 igraph_1.2.2 bitops_1.0-6 gtable_0.2.0 curl_3.2
[61] DBI_1.0.0 sets_1.0-18 R6_2.3.0 gridExtra_2.3 knitr_1.20
[66] bit_1.1-14 bindr_0.1.1 fastmatch_1.1-0 fgsea_1.8.0 readr_1.1.1
[71] stringi_1.2.4 Rcpp_1.0.0 piano_1.22.0 tidyselect_0.2.5
See https://hub.docker.com/r/bioconductor/bioconductor_docker to update the following line to use the appropriate Docker image:
Line 1 in d6be0a1
Hi I was going through the tutorial and ran into this error:
zscores <- loadCMapZscores(perts[ , 1:10])
Loading data from /home/shared/Misc_studies/CMap_DepMap/cmapZscores.gctx...
Error in .local(.Object, ...) : unused argument (verbose = verbose)
Pls advise. Thank you.
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