choishingwan PRS-Tutorial issues

choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis

MIT License

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issues

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Threshold and phenotypic variation values expectation from PRSice are wrong in the tutorial

#55 flaviaerius opened 1 month ago
1
Link to Base Data does not link to Google Drive

#54 AlexKoeppelSigSci opened 5 months ago
0
Confusion about pruning and clumping

#53 ptranvan closed 6 months ago
1
Not getting any plot

#52 SoumenMaity922 closed 6 months ago
1
LD-pred 2 issue, All NAs in PRS file

#51 ShoaibBME opened 1 year ago
1
LDpred 2 issue.

#50 ShoaibBME opened 1 year ago
0
Question On PRS.Best File

#49 SamGreen52 opened 1 year ago
0
Look into PRS components of each individual sample in PLINK --score?

#48 fzel1994 opened 1 year ago
0
make numbered list continue

#47 szcf-weiya closed 1 year ago
0
fix typo

#46 szcf-weiya closed 1 year ago
0
Base Data QC, no INFO score?

#45 Poppo9 closed 1 year ago
1
Missing Height.QC.gz file

#44 jzollner closed 2 years ago
2
Query regarding PRS

#43 singh-p closed 1 year ago
1
Genome build test

#42 fmadani closed 2 years ago
1
Question on PRS.summary file

#41 dzimmerman-amc closed 1 year ago
1
No 'SNP matching' in the Lassosum

#40 fmadani closed 1 year ago
7
No application for fam variable in the Lassosum

#39 fmadani closed 2 years ago
2
LDPred-2 error: N/A values for beta_grid in genomewide scenario

#38 fmadani closed 2 years ago
3
fam order dependency on chromosomes

#37 fmadani closed 2 years ago
0
number of chromosomes in the LDPred-2

#36 fmadani closed 2 years ago
1
LDPred-2 -- chromosome based LD Calculation

#35 fmadani closed 2 years ago
8
Hi, I am using the guidelines provided in your tutorial to calculate PGS in my dataset from already published PGS available in the catalogue. while in plink all runs well except for results are written in .*.profile. which I cannot find being created in my directory as described in your tutorial.

#34 MehreenSoomro closed 2 years ago
1
PRSice would calculate allele frequencies even if --maf is not there

#33 ptn24 closed 2 years ago
5
'y.col' and 'ind.col' should have the same length.

#32 Sandyyy123 closed 2 years ago
2
'ind.col' and 'rows_along(A.col)' should have the same length.

#31 Sandyyy123 closed 2 years ago
1
'ind.col' and 'rows_along(A.col)' should have the same length.

#30 Sandyyy123 opened 2 years ago
1
'y.col' and 'ind.col' should have the same length.

#29 Sandyyy123 closed 2 years ago
0
#mismatching-snps

#28 DM087 opened 2 years ago
9
Not able to reproduce the best fit PRS for plink

#27 ranijames opened 2 years ago
17
Hyperparameter Tuning with QC Tutorial

#26 jfrank94 closed 3 years ago
1
subsetting target dataset prior to analysis

#25 EugeneEA closed 3 years ago
2
File hm3_variants.rds removed by privefl

#24 mathieu-lemire closed 3 years ago
1
Correction for removing duplicated SNPs.

#23 MCorentin closed 3 years ago
2
Question on PRSice-2 section results & documentation

#22 james16292 opened 3 years ago
7
Error:No statistic column in file

#21 PyunJung-Min closed 3 years ago
4
Couple more spelling fixes.

#20 sammyjava closed 3 years ago
0
LDpred-2 tutorial: error in "Obtain model PRS"

#19 DM087 closed 3 years ago
14
Lassosum tutorial : Error in validation step

#18 DM087 closed 3 years ago
1
Question about validation set

#17 tengfeixiaozhu closed 3 years ago
4
Add Individual level PRS to .fam file

#16 XcodeBio closed 3 years ago
1
Error: Incompatibility between dimensions

#15 XcodeBio closed 3 years ago
11
a typo? map <- obj.bigSNP$map[-2]

#14 XcodeBio closed 3 years ago
2
plink parameters for generating PRS

#13 xcliu-oc opened 3 years ago
2
Confusion about "running PRS analysis" subsecion in PRSice-2 section

#12 MapleHe closed 3 years ago
1
Typo in "Update Effect Size" subsection in the section PLINK

#11 MapleHe closed 3 years ago
2
Error in calculating LD

#10 Qiaolan opened 3 years ago
5
plink argument for pruning wrong

#9 jhagenberg opened 3 years ago
1
a1/a0 in genotype file using the LDpred2 tutorial

#8 kaibios0101 closed 4 years ago
2
Typo in PLINK PRS calculation

#7 williamthistle closed 4 years ago
3
A small error in the QC Control code

#6 PradoVarathan closed 4 years ago
2