Error in ActivePathways in R
I am trying to find the pathways using ActivePathways R package. I am following this tutorial - https://github.com/reimandlab/ActivePathways
I wrote this code -
install.packages('ActivePathways')
devtools::install_github('https://github.com/reimandlab/ActivePathways', build_vignettes = TRUE)
library(ActivePathways)
setwd('/home/sanjana/Downloads/miten')
fname_scores <- system.file("extdata", "c - Sheet1.tsv", package = "ActivePathways")
fname_GMT <- system.file("extdata", "hsapiens_REAC_subset.gmt", package = "ActivePathways")
scores <- read.table(fname_scores, header = TRUE, row.names = 'Gene')
scores <- as.matrix(scores)
scores[is.na(scores)] <- 1
enriched_pathways <- ActivePathways(scores, fname_GMT)
I am encountering this error even thorugh I converted the dataframe into matrix-
Error in ActivePathways(scores, fname_GMT): scores must be a numeric matrix Traceback:1. ActivePathways(scores, fname_GMT) 2. stop("scores must be a numeric matrix")
• 1,369 views
•
link
updated
by
Matthias Zepper
•
written
by
Maliha •
•
written
by
Maliha •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Error in R: System command 'Rcmd.exe' failed
written by joonhong kwon •
-
Implementation of PreMSIm in R
written by a.basitkhan1990 •
-
Tool: driveR - Prioritizing Cancer Driver Genes Using Genomics Data
written by egeulgen
-
problem in installing Sleuth to Jupyter Notebok
written by ainulyaqin929 •
-
Co-Occurr Package (ggplot2 adjustments)
written by biohacker_tobe •
-
Deseq2 Single-Cell analysis with two variables
written by michele.tebaldi.92 •
-
MetaboAnalyst Install problems?
written by BeetleCheers •
-
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
written by egeulgen
-
How to read in count data from matrix of read counts into Deseq2
written by Wet&DryImmunology
-
R stat heatmap problem
written by sparrowquality •
Can you please show the output of
class(scores)andstr(scores)?the output of class(scores) is
The output of str(scores) is
Admittedly, I was quite confused, because data loaded with a command like the one above should always work. It loads the example dataset that ships with the package, so it is thoroughly tested - manually and in the meantime also usually via CI pipelines.
But then I realized you changed the file name from "
Adenocarcinoma_scores_subset.tsv" to "c - Sheet1.tsv". Evidently, you have to adhere to the names the package's authors give to their example data if you want to use that.If you actually want to run the analysis with your own data, you should load it separately and make sure that the result looks similar to the example data in terms of class, column names etc. Also, I recommend changing your filename, since "c - Sheet1.tsv" is dicey because of the blanks in there.