Hi,
I am trying to generate a structure file through PGDSpider, for a diploid organism, where each locus is in two consecutive columns in one row, rather than data for each individual be stored as 2 consecutive rows, where each locus is in one column (as mentioned as one option in structure format: https://web.stanford.edu/group/pritchardlab/software/structure22/readme.pdf). In the spid file, I defined: # What is the ploidy of the data?
VCF_PARSER_PLOIDY_QUESTION=DIPLOID_ONE_ROW (http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider%20manual_vers%202-1-1-5.pdf). However, the output still have each individuals be stored as 2 consecutive rows rather than in one row. Just wondering whether you have any suggestions for it.
Thanks,
Jia
Hi,
To answer the question I asked a bit earlier:
From my understanding, we could not generate a structure format with each locus in two consecutive columns in one row through PGDSpider directly. So instead, I used the following R script to convert
####before reading the table, we need to unify the separations in the txt. The original structure file generated by PGDSpider separated by both "\t" and " ".
all_loci=read.table("SNP_structure2.txt", header=TRUE, sep="")
#remove population column
all_loci_2=all_loci[,-2]
#all_loci_2
#split the odd and even entries of the rows
s2=split(all_loci_2, 1:2)
#rename column names
colnames(s2$'1')
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