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egeulgen / pathfindR

pathfindR: Enrichment Analysis Utilizing Active Subnetworks
https://egeulgen.github.io/pathfindR/
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csv file problem #30

Closed safrikDut closed 4 years ago

safrikDut commented 4 years ago

Hi! I´m having problems with reading the .csv file upon loading pathfindR.

read.csv (file) the environment shows me 1233 obs of 3 variables

or

glimpse (file)

Observations: 1,522 Variables: 3 $ gene_symbol IFNL1, IFNL3, IFNL2, IFNL4, EGR2, IFNB1, IFI44L, XAF1, GBP4, CXCL10, CCL5... $ logFC 13.36986141, 13.00849043, 12.87799430, 11.50148222, 11.09193259, 10.97011... $ pvalue 1.4602e-28, 5.9649e-27, 2.3935e-26, 3.6240e-21

but when using

suppressPackageStartupMessages(library(pathfindR))

data(file) head(file)

the environment shows 1233 obs of 1 variable and the table shows one one column with altogether: gene_symbol,logFC,pvalue

Could I get the file RA_input.csv as example to compare the format?

egeulgen commented 4 years ago

can you share the file? You may save the example input yourself via write.csv(RA_input, "file.txt"). I doubt that the package can interfere with read.csv()

safrikDut commented 4 years ago

Here is the file!

KAN1_allR.zip

I used Excel 2016 and saved it as .csv.

egeulgen commented 4 years ago

I cannot replicate your issue. Perhaps, it is related to another package or your OS? Is it still persisting? I am closing this issue as it does not seem to be related to pathfindR