User: aroso491

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aroso4910
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Posts by aroso491

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Comment: C: How to retrieve Gene name from SNP ID using biomaRt
... I know that it's been long since you answered this but I find myself in a similar position (your comments and solution were amazingly helpful, thanks) with a twist: when I use associated_gene attribute, I get a list with a simple few gene names here and there, very scattered, but I have manually che ...
written 9 days ago by aroso4910
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Comment: C: How to obtain the chromosomal location for a list of 8M SNPs?
... Thank you so much! This sounds exactly like what I needed. I am giving it a try right now, will let you know if it worked. :) Edit: It worked just fine, although it's only been able to retrieve 3.5 million out of my 8 million file. I assume this is normal as some of the SNPs might just not be in th ...
written 4 weeks ago by aroso4910
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How to obtain the chromosomal location for a list of 8M SNPs?
... Hello, I have a list of 8M SNPs from a meta-GWAS which does not include the chromosome ID and chromosome location in bp. I thought I could do this using the grch37.ensembl.org mart of bioMart (I have never done this before and I am still learning), but I have read in other posts that there is a 500 ...
vcf R biomart snp ensembl written 4 weeks ago by aroso4910
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Comment: C: Avoid repetition in script
... Yes, this is my dataframe ch1_SCPG. The columns are (ignoring the first column): ID CHR POSITION P STUDY_ID and the idea is that I will be able to do this for all chromosomes (1 to 22). I just don't see how can I loop it as it is a chunky piece of code and it confuses me. 1 cg16145216 1 423856 ...
written 5 weeks ago by aroso4910
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Avoid repetition in script
... Hello! I have a little script that allows me to create overlapped Manhattan plots with ggplot2 between 2 different dataframes (SNPs and CpGs). I have interesting columns in 22 chromosomes and intend to get 22 plots. However, I was thinking that repeating the same code over and over 22 times was a b ...
plotting R snp manhattan plot cpg written 5 weeks ago by aroso4910
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Comment: C: Loop to retrieve rsID out of chrID list
... This is much more elegant and simple, thank you! ...
written 5 weeks ago by aroso4910
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Comment: C: Loop to retrieve rsID out of chrID list
... Thanks! I got it sorted in the end, I didn't realize I was passing the whole column instead of going row by row... I ended up doing SSNP_M_Ch$CHR[i,2], SSNP_M_Ch$POS[i,3] and just added the index value as another column in temp and that worked smoothly. ...
written 6 weeks ago by aroso4910
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Comment: C: NGSseq heatmap RStudio
... I forgot to add that it worked perfectly in case anyone passes by and wonders if it was worth it or not. ...
written 6 weeks ago by aroso4910
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Loop to retrieve rsID out of chrID list
... Hello, I have a GWAS summary statistics file where some of the rows are not rsID but chrID. I want to use bioMart package in R in order to find all the rsIDs for my 232 chrIDs in this format: chr1_11105545 **1** **11105545** T C 0.965395 0.72017 -7.40832e-03 0.00460502 0.113547560 In bold the col ...
genome R biomart snp written 6 weeks ago by aroso4910 • updated 6 weeks ago by Mike Smith1.5k
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Comment: C: NGSseq heatmap RStudio
... That's brilliant, thank you, will try and let you know if it worked!! ...
written 4 months ago by aroso4910

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