User: sayyarsehrish

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Posts by sayyarsehrish

<prev • 22 results • page 1 of 3 • next >
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Comment: C: How to plot PCA figure using Genesis software?
... i have data in plink output format but i have no information about different groups in data output. ...
written 17 days ago by sayyarsehrish0
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How to plot PCA figure using Genesis software?
... I have generated PCA files using plink (eigenvec and eigenval). now I am trying to plot PCA figure using genesis software. but the figure doesn’t give me any information about group showing no group. how can I sort out this error. genesis need phenotype file and have no phenotype file. ...
pca genesis plink R written 24 days ago by sayyarsehrish0 • updated 24 days ago by zx87549.9k
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Comment: C: plotting PCA PLINK eigenvec output in R
... i have no PED data. how can i use this script for plotting PCA # read in the PED data PED <- read.table('20130606_g1k.ped', header = TRUE, skip = 0, sep = '\t') PED <- PED[which(PED$Individual.ID %in% rownames(eigenvec)), ] PED <- PED[match(rownames(eigenvec), PED$Individual.ID),] all(PED ...
written 28 days ago by sayyarsehrish0
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Comment: C: plotting PCA in R
... it give me error Error in read.table(plink2.eigenvec) : object 'plink2.eigenvec' not found > plot(ret_pca$PC1,ret_pca$PC2) ...
written 28 days ago by sayyarsehrish0
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plotting PCA PLINK eigenvec output in R
... I have obtained two files .eigenvec and .eigenval after executing the command --pca on PLINK 1.9. now how can i plot PCA in R package. is there any tutorial? any script ...
pca plink written 29 days ago by sayyarsehrish0 • updated 28 days ago by Kevin Blighe70k
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Comment: C: Principle component analysis using VCF file as input.
... also guide me how can now use egeinvec and eigen value in R for plotting pca ...
written 29 days ago by sayyarsehrish0
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Comment: C: Principle component analysis using VCF file as input.
... thanks it solved i have got two files eigenvec and eigen value. i am confused that my psm file have no sex(male female) information, will this create any bias in result? ...
written 29 days ago by sayyarsehrish0
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Comment: C: Principle component analysis using VCF file as input.
... please guide me. I have low knowledge about plink and PCA. ...
written 4 weeks ago by sayyarsehrish0
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Comment: C: Principle component analysis using VCF file as input.
... i use this command for PCA (plink2 --pfile file --PCA) it give me error failed to open .psam file. ...
written 4 weeks ago by sayyarsehrish0
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Comment: C: Principle component analysis using VCF file as input.
... I use pgen command it give me three files i.e. pgen, pvar, and psam. how can i use these file for plotting PCA. plz guide me further. --vcf: 4690 variants scanned. --vcf: NV-temporary.pgen + NV-temporary.pvar.zst + NV-temporary.psam written. 822 samples (0 females, 0 males, 822 ambiguous; 822 foun ...
written 4 weeks ago by sayyarsehrish0

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