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xinghuq / KLFDAPC

KLFDAPC: Kernel local Fisher discriminant analysis of principal components (KLFDAPC) for large genomic data
https://xinghuq.github.io/KLFDAPC/
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Input files explanation required #4

Closed raveancic closed 2 years ago

raveancic commented 2 years ago

Thanks for this tool. Unfortunately I did not find a clear explanation on which format the tool accept as input/how to create the .gds. I think this can be really useful for reproducibility with other data set.

xinghuq commented 2 years ago

Hi, thanks for your feedback, I just updated the explanation in readme file:

GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. Details can be found here.

You can convert PLINK/Oxford files to GDS using SNPRelate (Zheng et al. 2012).

snpgdsBED2GDS Conversion from PLINK BED to GDS. snpgdsGEN2GDS Conversion from Oxford GEN format to GDS. snpgdsPED2GDS Conversion from PLINK PED to GDS

Below, is an example on how to convert PLINK bed files to GDS,

library("SNPRelate")
# PLINK BED files
bed.fn ="/file_location/target.bed"
fam.fn = "/file_location/target.fam"
bim.fn = "/file_location/target.bim"

# convert
snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "HapMap.gds")

# open
genofile <- snpgdsOpen("HapMap.gds")
genofile

# close
snpgdsClose(genofile)

On Fri, 3 Jun 2022 at 17:56, Alessandro Raveane @.***> wrote:

Thanks for this tool. Unfortunately I did not find a clear explanation on which format the tool accept as input/how to create the .gds. I think this can be really useful for reproducibility with other data set.

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raveancic commented 2 years ago

Super Thanks!