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Aditya Saxena
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10
@aditya-saxena-6706
Last seen 6.4 years ago
I am facing an strange error while using SPIA function through ToPASeq package
> library(ToPASeq) > expr<-read.csv("gcrma.csv") > rownames(expr)<-expr$EG > expr$EG<-NULL > expr$Symbols<-NULL > expr<-as.matrix(expr) > class<-read.csv("disease.csv") > disease<-class$disease > names(disease)<-as.vector(class$sample) > pathways<-pathways("hsapiens", "kegg")[1:10] > spi<-SPIA(expr, disease, pathways , type="MA", logFC.th=-1) Error in SPIA(expr, disease, pathways, type = "MA", logFC.th = -1) : could not find function "SPIA"
my session information is:
R version 3.5.0 (2018-04-23) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8.1 x64 (build 9600) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] ToPASeq_1.14.0 graphite_1.26.1 loaded via a namespace (and not attached): [1] Rcpp_0.12.17 IRanges_2.14.10 digest_0.6.15 [4] rappdirs_0.3.1 R6_2.2.2 DBI_1.0.0 [7] backports_1.1.2 stats4_3.5.0 RSQLite_2.1.1 [10] graph_1.58.0 httr_1.3.1 blob_1.1.1 [13] S4Vectors_0.18.3 checkmate_1.8.5 bit64_0.9-7 [16] Biobase_2.40.0 bit_1.1-14 parallel_3.5.0 [19] compiler_3.5.0 BiocGenerics_0.26.0 AnnotationDbi_1.42.1 [22] memoise_1.1.0
Kindly let me know how to rectify it