flashpca-users

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Welcome to flashpca-users!

This is a place for users of flashpca to ask questions, discuss bugs, and ask new for features related to flashpca (https://github.com/gabraham/flashpca).

When asking for help, please specify:
- Operating System
- Whether it's flashpca or flashpcaR, and version
- R version, if used

0 selected

1/18/23

Question about installing Flashpca

Hi all, I am trying to install flashpca in Linux. When I run make all, I encountered the following

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Question about installing Flashpca

Hi all, I am trying to install flashpca in Linux. When I run make all, I encountered the following

1/18/23

Daniel Bontempo2

1/7/22

Installing on Windows

I am running R 4.1.2 on a Windows 8.1 system. I want to have flashpcaR so I can see the speed and

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Installing on Windows

I am running R 4.1.2 on a Windows 8.1 system. I want to have flashpcaR so I can see the speed and

1/7/22

11/4/21

Installing flashpca with conda

Dear all, Is there a way to install flashpca using conda? By following the way specified on github,

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Installing flashpca with conda

Dear all, Is there a way to install flashpca using conda? By following the way specified on github,

11/4/21

9/16/21

check accuracy with the mean squared error

Hi there, Thank you for sharing this excellent tool. I am a new user of flashpca and would like to

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check accuracy with the mean squared error

Hi there, Thank you for sharing this excellent tool. I am a new user of flashpca and would like to

9/16/21

Tobias Wolfram, Gad Abraham2

6/29/21

Expected Runtime for 550k SNPs, 500k Respondents and 100 PCs

Hi Tobias, Thanks for your message. Hard to say without the details of your workstation, but two

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Expected Runtime for 550k SNPs, 500k Respondents and 100 PCs

Hi Tobias, Thanks for your message. Hard to say without the details of your workstation, but two

6/29/21

Ana Marija, Gad Abraham2

10/8/19

how to use FlashPCA2 with my Plink2 GWAS Pipeline

Hi Ana, Maybe I'm misunderstanding but you probably should do QC on each chromosome 1-22 (as you

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how to use FlashPCA2 with my Plink2 GWAS Pipeline

Hi Ana, Maybe I'm misunderstanding but you probably should do QC on each chromosome 1-22 (as you

10/8/19

8/15/19

Correspondence between plink .fam file IIDs and flashpca output

Hi, I'm a user of the R version of flashpca. I used plink file as the input for the flashpca()

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Correspondence between plink .fam file IIDs and flashpca output

Hi, I'm a user of the R version of flashpca. I used plink file as the input for the flashpca()

8/15/19

Carlos Sarabia, Gad Abraham2

7/29/19

fatal error: program_options.hpp not found. Installation problem

Hi Carlos, You boost paths look a bit different to mine, on both Linux Ubuntu 12.04 and MacOS 10.14 I

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fatal error: program_options.hpp not found. Installation problem

Hi Carlos, You boost paths look a bit different to mine, on both Linux Ubuntu 12.04 and MacOS 10.14 I

7/29/19

7/16/19

Fixing compatibility with RSpectra/Spectra

Hi all, The latest development version of flashpca on github (https://github.com/gabraham/flashpca)

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Fixing compatibility with RSpectra/Spectra

Hi all, The latest development version of flashpca on github (https://github.com/gabraham/flashpca)

7/16/19

Luca Albergante, … Nicole Torosin11

5/13/19

Fraction of explained variance in the R function

Hi Gad, I found these and have gotten that to work, thank you! Nicole On Wednesday, May 8, 2019 at 10

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Fraction of explained variance in the R function

Hi Gad, I found these and have gotten that to work, thank you! Nicole On Wednesday, May 8, 2019 at 10

5/13/19

Mitja Mitrovic, Gad Abraham2

5/9/19

Can't produce loadings

Hi Mitja, Are you running the most recent version? Gad On Wed, 8 May 2019 at 04:41, Mitja Mitrovic

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Can't produce loadings

Hi Mitja, Are you running the most recent version? Gad On Wed, 8 May 2019 at 04:41, Mitja Mitrovic

5/9/19

Chinh Nguyen, Nicole Torosin2

5/6/19

Problem with installing

Hi Chinh, I had the exact same issue that I have not been able to figure out how to fix. Nicole On

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Problem with installing

Hi Chinh, I had the exact same issue that I have not been able to figure out how to fix. Nicole On

5/6/19

Nicole Torosin, Gad Abraham4

1/2/19

How does flashpca handle missing data

Hi Nicole, It really depends on what you're trying to do; if you want to detect population

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How does flashpca handle missing data

Hi Nicole, It really depends on what you're trying to do; if you want to detect population

1/2/19

Remi Daviet, Gad Abraham2

12/11/18

Cannot manage to install flashpcaR on Windows

Hi Remi, The Windows zip is not actually a source package, it's a precompiled package. Can you

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Cannot manage to install flashpcaR on Windows

Hi Remi, The Windows zip is not actually a source package, it's a precompiled package. Can you

12/11/18

Nicole Torosin, Gad Abraham6

9/19/18

flashPCAR cannot load .fam file

Nicole, these would be the per-SNP loadings, to get these you'll need to re-run flashpca with

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flashPCAR cannot load .fam file

Nicole, these would be the per-SNP loadings, to get these you'll need to re-run flashpca with

9/19/18

chelsie benca, Gad Abraham2

8/9/18

FlashPCA2 not multithreading

Hi Chelsie, In v2, the flashpca multithreading probably won't help much because what it does is

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FlashPCA2 not multithreading

Hi Chelsie, In v2, the flashpca multithreading probably won't help much because what it does is

8/9/18

5/9/18

mitochondrial/haploid SNPs PCA

Hi, I have a large scale dataset from biobank and wanted to calculated mtPCA can flash PCA take plink

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mitochondrial/haploid SNPs PCA

Hi, I have a large scale dataset from biobank and wanted to calculated mtPCA can flash PCA take plink

5/9/18

Palvi Malik, Gad Abraham2

2/20/18

Not able to run flashPCAR

fn is the path to your plink data, eg, if your plink files are data.bed, data.bim, data.fam, then fn

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Not able to run flashPCAR

fn is the path to your plink data, eg, if your plink files are data.bed, data.bim, data.fam, then fn

2/20/18

11/23/17

Re: Cannot project new individuals onto existing PCs

Hi, For project(), you need to give the root name of the PLINK data (not a directory), similar to how

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Re: Cannot project new individuals onto existing PCs

Hi, For project(), you need to give the root name of the PLINK data (not a directory), similar to how

11/23/17

aq teha, … Gad Abraham4

11/7/17

Cant install flashpcaR in r.

It sounds like you don't have the R development tools installed, perhaps you need https://cran.r-

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Cant install flashpcaR in r.

It sounds like you don't have the R development tools installed, perhaps you need https://cran.r-

11/7/17

Vince Forgetta, Gad Abraham3

9/25/17

flashPCA2 v PLINK2 pca approx

Hi Vince, Did you solve this issue? Gad On Thursday, 10 August 2017 18:50:11 UTC+1, Vince Forgetta

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flashPCA2 v PLINK2 pca approx

Hi Vince, Did you solve this issue? Gad On Thursday, 10 August 2017 18:50:11 UTC+1, Vince Forgetta

9/25/17

Wei-Yu Lin, Gad Abraham2

9/25/17

flashPCA2 (make: *** [flashpca.o] Error 1)

Hi Wei-Yu, Did you manage to solve this? Gad On Wednesday, 19 July 2017 10:37:31 UTC+1, Wei-Yu Lin

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flashPCA2 (make: *** [flashpca.o] Error 1)

Hi Wei-Yu, Did you manage to solve this? Gad On Wednesday, 19 July 2017 10:37:31 UTC+1, Wei-Yu Lin

9/25/17

Chunkao Wang, Gad Abraham2

5/25/17

How can I got PCs (principle components) from flashpcaR

Hi Chunkao, The 'projection' matrix is the PCs (column 1 is PC1, column 2 is PC2, etc). Gad

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How can I got PCs (principle components) from flashpcaR

Hi Chunkao, The 'projection' matrix is the PCs (column 1 is PC1, column 2 is PC2, etc). Gad

5/25/17

5/18/17

FlashPCA2 paper published in Bioinformatics

A paper describing FlashPCA2 has been published at https://doi.org/10.1093/bioinformatics/btx299 (

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FlashPCA2 paper published in Bioinformatics

A paper describing FlashPCA2 has been published at https://doi.org/10.1093/bioinformatics/btx299 (

5/18/17

Vince Forgetta, Gad Abraham4

4/6/17

Harmonize EIGENSTRAT results with flashpca

In discussion with Gad via email, we found that outlier removal while using EIGENSTRAT was the issue.

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Harmonize EIGENSTRAT results with flashpca

In discussion with Gad via email, we found that outlier removal while using EIGENSTRAT was the issue.

4/6/17

12/21/16

New release: FlashPCA2

FlashPCA2 is a new release of FlashPCA, replacing the previous randomised algorithm with the

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New release: FlashPCA2

FlashPCA2 is a new release of FlashPCA, replacing the previous randomised algorithm with the

12/21/16

Florian Privé, Gad Abraham7

12/3/16

Are we sure of accuracy of the scores/loadings?

I get something similar indeed. I fear that randomized PCA gets more inaccurate with larger samples.

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Are we sure of accuracy of the scores/loadings?

I get something similar indeed. I fear that randomized PCA gets more inaccurate with larger samples.

12/3/16

9/12/16

Upcoming new release of FlashPCA

An 'alpha' version of FlashPCA 2.0 is available at https://github.com/gabraham/flashpca/tree/

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Upcoming new release of FlashPCA

An 'alpha' version of FlashPCA 2.0 is available at https://github.com/gabraham/flashpca/tree/

9/12/16

LME, Gad Abraham5

6/7/16

projection difference between XV and UD

There are three issues here: 1) By default, flashpca computes the eigen-decomposition of X^TX / (n -

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projection difference between XV and UD

There are three issues here: 1) By default, flashpca computes the eigen-decomposition of X^TX / (n -

6/7/16

aq teha, Gad Abraham4

5/11/16

Then r$vectors are the eigenvectors, and r$values are the eigenvalues. Please look at help via ?

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Then r$vectors are the eigenvectors, and r$values are the eigenvalues. Please look at help via ?

5/11/16

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