Error in path.expand(path) : invalid 'path' argument

[Suzana Ezquina]

Hello, Shawn!

I need help using SKAT.

I have done my binary PLINK files from the VCF, used PLINK to generate the file.SetID.

I entered the files with the "read.table" function and used MultiPhen to enter the bed file into R, using the "read.plink" function.

I updated R to the version 3.2.2 and installed the package SKAT again, using the version 1.1.2 now.

I have permission to write in every file and folder I am using.

Now, I am stuck in the command Generate_SSD_SetID(bedfile, bimfile, famfile, setfile, File.SSD, File.Info) I don´t know what could be going wrong.

I understood I use my bedfile, bimfile, famfile, setfile and the function Generate_SSD_SetID will generate the file.SSD and File.Info. Is that correct?

I always get the error "Error in path.expand(path) : invalid 'path' argument", whith my files and even with the example files from this discussion group. I tried both the binary and the "Example1" files.

Is there another way to produce the File.SSD and File.Info?

Please help me, I have no more clues.

Thanks in advance

Suzana

[Seunggeun (Shawn) Lee]

Hi Suzana,

Can you send me your code to run Generate_SSD_SetID, so I can take a look whether there is any error?

Thanks,

Shawn

[Elisabetta Casalone]

Hello,

I got the same issue. How did you fix it?

Thanks,

Elisabetta

[Seunggeun (Shawn) Lee]

Hi Elisabetta, 

Can you show me your code so I can check whether there is any error in a file name?

Thanks,

Shawn

[Q]

Hello,

I got the similar issue, but the error is : Error in path.expand(path) : object 'WGS_coding_rare_temp.bed' not foundype=TRUE)

Please help me

Thank you 

[Seunggeun (Shawn) Lee]

Hi,

I am very sorry for the late response. Not sure why you have this error. 

If you still have this problem, can you provide me the code?

Thanks,
Shawn

[Yiming Luo]

Hello Shawn,

I have the exact same problem with "Error in path.expand(path) : invalid 'path' argument" and wonder if you can help me. The code I have the as following:

install.packages("Matrix")

install.packages("SPAtest")

install.packages("SKAT")

if (!requireNamespace("BiocManager", quietly = TRUE))

  install.packages("BiocManager")

BiocManager::install("snpStats")

library(Matrix)

library(SPAtest)

library(SKAT)

library(snpStats)

rp <- read.plink("BED.bed", "BED.bim", "BED.fam", na.strings = c("0", "-9"), sep = "." , select.subjects = NULL, select.snps = NULL)

bed=as.data.frame(rp$genotypes)

fam=as.data.frame(rp$fam)

bim=as.data.frame(rp$map)

File.SetID<-read.table("File.SetID ")

 
Generate_SSD_SetID(File.Bed = bed, File.Bim = bim, File.Fam = fam, File.SetID = File.SetID,File.SSD = "SSD",File.Info = "info", Is.FlipGenotype=TRUE)

Thank you very much for your attention!

Yiming Luo

[Seunggeun (Shawn) Lee]

Hi Yiming,

bed, bim, fam, File.SetID should be file names. For example File.bed="BED.bed"

Thanks,
Shawn

2020년 10월 6일 화요일 오후 11시 46분 23초 UTC+9에 luoyim...@gmail.com님이 작성: