Error in file(file, "rt") : invalid 'description' argument
Hi, Please advise me to fix the following error while running the R script using ballgown for DGE analysis.
getwd()
[1] "/fast/users/a123456/prrdata"
pheno_data <- read.csv("pardge_phenotype.csv")
bg_par <- ballgown(dataDir = "prrdata", samplePattern = "sample", pData = pheno_data)
Fri Jan 12 09:58:30 2018
**Fri Jan 12 09:58:30 2018: Reading linking tables
Error in file(file, "rt") : invalid 'description' argument**
pheno_data()
Error in pheno_data() : could not find function "pheno_data"
pheno_data
ids treatment genotype
1 sample01 control High Resistance
2 sample02 control High Resistance
3 sample03 control High Resistance
4 sample04 control Moderate Resistance
5 sample05 control Moderate Resistance
6 sample06 control Moderate Resistance
7 sample07 control Susceptible
8 sample08 control Susceptible
9 sample09 control Susceptible
10 sample10 inoculated High Resistance
11 sample11 inoculated High Resistance
12 sample12 inoculated High Resistance
13 sample13 inoculated Moderate Resistance
14 sample14 inoculated Moderate Resistance
15 sample15 inoculated Moderate Resistance
16 sample16 inoculated Susceptible
17 sample17 inoculated Susceptible
18 sample18 inoculate
Thanks
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Kevin Blighe
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amy16 •
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Dear Amy,
I don't have a lot of experience with ballgown, but I think you need to run the script from the parent directory "/fast/users/a123456", while your data files must be in prrdata.
Thanks .... It worked!!!!