search

xiaolei-lab / rMVP

:postbox: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
Apache License 2.0
262 stars 69 forks source link

If i have genotype data in Numeric format, do I need to adjust the order of genotype file to be consistent with phenotype and map file? #62

Open biolittleboy opened 3 years ago

biolittleboy commented 3 years ago

Hi, Dr. Liu. I am running Gene-PAV-GWAS. All files need to be generated manually. Does the order of the rows of the ‘Numeric.txt’ and ‘Map.txt’ files need to be consistent? and does the order of the columns of the ‘Numeric.txt’ file need to be consistent with the order of the rows of the ‘Phenotype.txt’ file? Thanks in advance for the help.

hyacz commented 3 years ago

Yes, they need to be consistent. One row of the genotype file represents a marker, and one column represents an individual. The order of the rows needs to be the same as the map file, and the order of the columns needs to be the same as the phenotype file. You can check https://github.com/xiaolei-lab/rMVP#numeric for detailed instructions