PCA with split up chromosomes
Hi all,
Is there a way to do PCA with split up chromosome files? My files are too big to keep as a single bed/bim/fam but wanted my PCs for all chromosomes collectively instead of split up.
Thanks!
• 1,580 views
•
link
written
by
gradstudentNew •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
VCF to Plink files
written by hi.there •
-
Merge only bim files with plink
written by mgdrnl •
-
How to input multiple bed files in plink
written by Ruocheng •
-
Calculating polygenic score using plink
written by m.shoaib •
-
Split plink files from multiallelic to biallelic
written by MAPK
-
LD calculation with plink
written by naghme.vahabi94 •
-
PLINK2 and data split by chromosomes
written by bigfoot •
-
Looping over plink files
written by paolo002
-
Split plink files by a number of SNPs
written by kakukeshi
-
PLINK: merge .bed files
written by bsmith030465
PCA should be run after you've applied a MAF filter and performed LD pruning (e.g. --indep-pairwise). If per-chromosome bed/bim/fam files are small enough to be usable at the beginning, a merged all-chromosome bed/bim/fam is almost always small enough to be usable after MAF filtering and LD pruning.
@chrchang523, is this true even for bgens containing 500k or more samples?