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choishingwan
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PRS-Tutorial
A tutorial on how to run basic polygenic risk score analysis
MIT License
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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
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