example data input file help!

[krkim1989]

I am a beginner in RAINBOWR.

1536 SNP set was downloaded, and the downloaded data was

data("Rice_Zhao_etal") Rice_geno_score <- Rice_Zhao_etal$genoScore Rice_geno_map <- Rice_Zhao_etal$genoMap Rice_pheno <- Rice_Zhao_etal$pheno Rice_haplo_block <- Rice_Zhao_etal$haploBlock

I entered it, but

See(Rice_geno_score) See(Rice_geno_map) See(Rice_pheno) See(Rice_haplo_block)

After entering

[1] "class: NULL" [1] "dimension: " Warning message: In See(Rice_geno_map): We cannot offer the simple view of your data. Instead we will offer the structure of your data. NULL

Can you tell me in detail how to create an input file, or if there is an extension name or input file that I don't know? I want to use RAINBOWR, but I can't keep using it. help me!!

[KosukeHamazaki]

Did you load the RAINBOWR package to R? Please show all the scripts and error codes you have. Also, please tell me the R and RAIBOWR version.

As for the input file, please refer to the example dataset, which can generally be read from csv/tsv files. Also, for the marker genotype data, please tell me what kind of dataset you have. (e.g., vcf, plink, ... format)

[krkim1989]

Zhao_et_al.map.txt Zhao_et_al.ped.txt Zhao_et_al.txt

A total of 3 example files were used. Is it possible to test with this file?

[KosukeHamazaki]

I think you are using the plink format, right? First, please convert it to a vcf file by referring to here. Then, after getting a vcf, please extract the GT score and convert it to a csv/tsv file by referring to here (Japanese page, please translate it into English).

Finally, you can read it into R by the read.csv function.