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Quality Control in SPS data in R

问题描述:

I have a big dataset with SNPs (genotypes) which is 501 rows and 42844 columns.

The data is like that :

 OAR19_64675012.1 OAR19_64803054.1 OAR1_88143.1 s09912.1 s36301.1 s34880.1

AB AB BB BB AA AA

AB AB AB AA AB AB

AB AB BB AB BB AA

AA BB BB AB AA AA

I have a big problem in the QC process.

I'm using the QCGWAS library in R and when I'm hitting the command in order to start Quality Control:

 headers<- names(snp) ## names of the columns, snp is the dataframe above

# make them as a dataframe with characters

h_data<- as.character(data.frame(headers , stringsAsFactors = F))

new_data <- QC_GWAS(filename = "data1.txt", # command for QC data1.txt is my snps data

header_translations = h_data,

save_final_dataset = TRUE)

I'm getting an this Error :

Error: file.exists(paste(dir_references, header_translations, sep = "/")) is not TRUE

I don't know what i have to do.... I'm searching things but i'm getting errors all the time... I try to follow the quick start guide in /R/library/QCGWAS/doc but i'm getting Errors.

Please if anyone has an idea and some time to help me i would apreceate that. It is very significant for me to solve this problem in order to continue the project. I've used some other libraries but I couldn't handle the quality control because they didn't give me clean data.

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