I have a VCF file containing genotype date for a few thousand SNPs across a few thousand samples. I would like to firstly convert this to a matrix (possibly using the VariantAnnotation package) and then perform a PCA analysis on the samples followed by some sort of clustering algorithm. I have very little experience with any of SNP matrix packages, PCA or clustering algorithms so I was wondering if anyone knew of any good tutorials which may be able to help me.
It is also worth noting that due to the nature of the analysis I am running, the SNP matrix will be extremely sparse. I would therefore also like to get information on the fraction of missing genotypes for each sample and the fraction of missing samples for each SNP - is this possible?
•
written
by
dominicdhall •
1 answer
Log in to answer this question.
-
PCA interpretation
written by nuriagaralon •
-
Plot PCA for .IMISS file?
written by Carla Hazel •
-
Batch effect correction without detecting any clustering on batches
written by SHN •
-
How to apply Robust PCA to SNP (HapMap) data?
written by Dhara Awasthi •
-
PCA analysis for beginners
written by Bella_p
-
Probabilistic PCA on very sparse SNP matrix
written by dominicdhall •
-
Creating a cell by SNP matrix
written by dominicdhall •
-
How to clustering people or base pair composition of snps?
written by xingshunkai •
-
matrixEQTL giving discrete p value distribution for SNP-Phenotype pairs
written by lc574 •
-
Is 1000 genomes data good enough to use for PCA?
written by das2000sidd •
