Closed SalimMegat closed 4 years ago
https://github.com/LieberInstitute/brainseq_phase2/tree/master/twas/reference_hg38 Is that what you are looking for?
Hi,
I guess that's the code to update the positions but we do not have access to the file "BrainSeq_Phase2_RiboZero_Genotypes_n551.rda" So what I was looking for would be more like a map that would look like this (attached) but that would contain your rsID of course. That way I would be able to filter my LD set accordingly.
Thank you,
Hi,
The BrainSeq_Phase2_RiboZero_Genotypes_n551.rda
file is part of the brainseq_phase2_genotypes
Globus collection we have at http://research.libd.org/globus/. You have to request access to the genotype data first, then send us your Globus email so we can give you access to the collection, after which you can then download the Rda file you are looking for.
Best, Leonardo
Here's a preview of the objects inside that .rda
file:
> load("BrainSeq_Phase2_RiboZero_Genotypes_n551.rda", verbose = TRUE)
Loading objects:
mds
snp
snpMap
> head(snpMap)
CHR SNP CM POS COUNTED ALT Type
rs9988021:866319:G:A 1 rs9988021:866319:G:A 0 866319 G A SNV
rs111819742:868861:C:T 1 rs111819742:868861:C:T 0 868861 T C SNV
GA018352 1 GA018352 0 879687 T C SNV
rs3748592 1 rs3748592 0 880238 A G SNV
rs2340582 1 rs2340582 0 882803 A G SNV
rs4246503 1 rs4246503 0 884815 A G SNV
newRef newCount name rsNumGuess chr_hg38
rs9988021:866319:G:A A G rs9988021 rs9988021 chr1
rs111819742:868861:C:T C T rs111819742 rs111819742 chr1
GA018352 C T rs2839 rs2839 chr1
rs3748592 G A rs3748592 rs3748592 chr1
rs2340582 G A rs2340582 rs2340582 chr1
rs4246503 G A rs4246503 rs4246503 chr1
pos_hg38
rs9988021:866319:G:A 930939
rs111819742:868861:C:T 933481
GA018352 944307
rs3748592 944858
rs2340582 947423
rs4246503 949435
> dim(snpMap)
[1] 7023860 13
> dim(snp)
[1] 7023860 551
> snp[1:5, 1:5]
Br5168 Br5073 Br5217 Br5234 Br5372
rs9988021:866319:G:A 0 0 0 0 1
rs111819742:868861:C:T 0 0 0 0 0
GA018352 1 0 0 0 1
rs3748592 0 0 0 0 1
rs2340582 0 0 0 0 1
Hi Leonardo,
Thank you for your reply ! I am totally aware that accessing the raw genotype data need to be requested through dbGaP as they are sensitive. However, I actually do not need to get access to the individual-level genotype data. I would only need the first part of the file that contain the list of the variants with position on hg19 and hg38. With this , I would be able to filter and update my LD set to hg38 positions and use the weights that you kindly provided. Do you think that it would be possible for you to share the first part with the mapping position only ?
I appreciate your help !
Best,
Salim.
Le 21 juil. 2020 à 17:27, Leonardo Collado-Torres notifications@github.com a écrit :
Here's a preview of the objects inside that .rda file:
load("BrainSeq_Phase2_RiboZero_Genotypes_n551.rda", verbose = TRUE) Loading objects: mds snp snpMap head(snpMap) CHR SNP CM POS COUNTED ALT Type rs9988021:866319:G:A 1 rs9988021:866319:G:A 0 866319 G A SNV rs111819742:868861:C:T 1 rs111819742:868861:C:T 0 868861 T C SNV GA018352 1 GA018352 0 879687 T C SNV rs3748592 1 rs3748592 0 880238 A G SNV rs2340582 1 rs2340582 0 882803 A G SNV rs4246503 1 rs4246503 0 884815 A G SNV newRef newCount name rsNumGuess chr_hg38 rs9988021:866319:G:A A G rs9988021 rs9988021 chr1 rs111819742:868861:C:T C T rs111819742 rs111819742 chr1 GA018352 C T rs2839 rs2839 chr1 rs3748592 G A rs3748592 rs3748592 chr1 rs2340582 G A rs2340582 rs2340582 chr1 rs4246503 G A rs4246503 rs4246503 chr1 pos_hg38 rs9988021:866319:G:A 930939 rs111819742:868861:C:T 933481 GA018352 944307 rs3748592 944858 rs2340582 947423 rs4246503 949435 dim(snpMap) [1] 7023860 13 dim(snp) [1] 7023860 551 snp[1:5, 1:5] Br5168 Br5073 Br5217 Br5234 Br5372 rs9988021:866319:G:A 0 0 0 0 1 rs111819742:868861:C:T 0 0 0 0 0 GA018352 1 0 0 0 1 rs3748592 0 0 0 0 1 rs2340582 0 0 0 0 1 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/LieberInstitute/brainseq_phase2/issues/33#issuecomment-661929722, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKO24HU4MKIFMJQKQM332E3R4WXVHANCNFSM4O57SESQ.
Hi,
We are in the process of uploading a text file with this data to AWS. You should be able to read it into R using read.table()
without any arguments.
## Test run
> write.table(head(snpMap), file = "BrainSeq_Phase2_RiboZero_Genotypes_n551_snpMap.txt", quote = FALSE)
> read.table("BrainSeq_Phase2_RiboZero_Genotypes_n551_snpMap.txt")
CHR SNP CM POS COUNTED ALT Type
rs9988021:866319:G:A 1 rs9988021:866319:G:A 0 866319 G A SNV
rs111819742:868861:C:T 1 rs111819742:868861:C:T 0 868861 T C SNV
GA018352 1 GA018352 0 879687 T C SNV
rs3748592 1 rs3748592 0 880238 A G SNV
rs2340582 1 rs2340582 0 882803 A G SNV
rs4246503 1 rs4246503 0 884815 A G SNV
newRef newCount name rsNumGuess chr_hg38
rs9988021:866319:G:A A G rs9988021 rs9988021 chr1
rs111819742:868861:C:T C T rs111819742 rs111819742 chr1
GA018352 C T rs2839 rs2839 chr1
rs3748592 G A rs3748592 rs3748592 chr1
rs2340582 G A rs2340582 rs2340582 chr1
rs4246503 G A rs4246503 rs4246503 chr1
## Creating th emain file
> Sys.time(); write.table(snpMap, file = "BrainSeq_Phase2_RiboZero_Genotypes_n551_snpMap.txt", quote = FALSE); Sys.time()
[1] "2020-07-21 13:08:49 EDT"
[1] "2020-07-21 13:09:49 EDT"
> system("wc -l *snpMap.txt")
7023861 BrainSeq_Phase2_RiboZero_Genotypes_n551_snpMap.txt
## Compress to save space
$ gzip BrainSeq_Phase2_RiboZero_Genotypes_n551_snpMap.txt
$ ls -lh
-rwxrwx--- 1 lcollado lieber_jaffe 165M Jul 21 13:09 BrainSeq_Phase2_RiboZero_Genotypes_n551_snpMap.txt.gz
Best, Leo
Hi Leonardo,
Many thanks for your help !!
Best,
Salim.
Le ven. 17 juil. 2020 13:47, Andrew Jaffe notifications@github.com a écrit :
https://github.com/LieberInstitute/brainseq_phase2/tree/master/twas/reference_hg38 Is that what you are looking for?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/LieberInstitute/brainseq_phase2/issues/33#issuecomment-660063825, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKO24HRSV2UM4GAWV7TKS3LR4A25BANCNFSM4O57SESQ .
Hi,
Thanks for sharing your TWAS weights ! I was wondering whether which map did you use to port LD set to hg38 coordinates ? I am also doing TWAS analysis in hg38 format but I have a lot of missing data when performing the TWAS with your weigth and my LD set updated to hg38. Would you ming sharing the updated LDset or give me a hint on which map you used for the conversion ?
I really appreciate your help !
Many thanks,
Salim.