SPIA function error in ToPASeq
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Entering edit mode
@aditya-saxena-6706
Last seen 3.4 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 

 

 

 

topaseq • 378 views
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Entering edit mode
@federico-marini-6465
Last seen 7 months ago
Germany

AFAIK ToPASeq does not load SPIA, so it seems normal that the function is not available.

library(SPIA)

could do the job?

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