How to extract a list of SNPs from summary data according to p-value in R?

Question

I have a GWAS data summary results that have the following information and want to extract a list of first 120 SNPs according to p-value in R. The data have following seven headers:

SNPName    n_samplesize    A1Allele    A2Allele    beta     SE      p_value

Code via dplyr:

    library(dplyr)
    dat <- read.csv(file.choose(MetaAnalysis_Results))
    dat2 <- dat %>% arrange("p_value")

The error occurred at sorting

Update: This worked for me after converting the .csv to .txt file

    attach(MetaAnalysis_Results)
    mydata <- MetaAnalysis_Results
    new <- mydata[order(p_value),]

Something like `head(myData[ order(myData$p_value), "SNPName" ], n = 120)` — zx8754, Mar 28 '19 at 11:38
@zx8754: This seems to be working but how do I do it if I want SNP list according to lowest to higher p-value? — Tabbi, Mar 28 '19 at 11:50

Omar113 · Accepted Answer · 2019-03-28T12:29:40.683

0

the easiest way to do this is to use dplyr. Install it if not existed

install.packages("dplyr")

    library(dplyr)
    dat <- read.csv(file.choose())

    #Make sure the data is imported
    head(dat)

    dat <- dat %>% arrange("p_values")
    dat2 <- dat[1:120,]
    write.csv(dat2)

edited Mar 28 '19 at 12:29

answered Mar 28 '19 at 11:31

Omar113

198
7

It is a .csv file downloaded directly from the web, and I want to extract a list of first 120 SNPs in a separate file along with other information (seven variables) according to lowest to the higher p-value. – Tabbi Mar 28 '19 at 11:40
check the update – Omar113 Mar 28 '19 at 11:48
We should order then subset. – zx8754 Mar 28 '19 at 11:54
I think he wants to select the first 120 first then subset! – Omar113 Mar 28 '19 at 12:00
1

@Omar113 I want 120 sorted by decreasing to increasing p-value – Tabbi Mar 28 '19 at 12:02
can you get clear. Do you want to sort the first 120 occurance or do you want to sort the whole dataset then subset the smallest 120 ? – Omar113 Mar 28 '19 at 12:07
Sorry! want to sort the whole dataset and then subset smallest 120. – Tabbi Mar 28 '19 at 12:14
The data in total have 2450547 SNPs and I tried to sort and then subset and getting this error: Error in arrange_impl(.data, dots) : incorrect size (1) at position 1, expecting : 2450547 – Tabbi Mar 28 '19 at 12:15
can you edit the post and include the code you have tried? – Omar113 Mar 28 '19 at 12:21
@Omar113 I've added the code I used in my original question plz – Tabbi Mar 28 '19 at 12:27
I have edited my code. Don't put anything in file.choose() , you will get a pop-up to choose the file from! – Omar113 Mar 28 '19 at 12:30
@Omar113: Data imported correctly but giving the same error after the 'arrange' command! – Tabbi Mar 28 '19 at 12:44
@Tabbi Can you share the head(dat) output? – Omar113 Mar 28 '19 at 16:00
@Omar113 Thank you. I updated my original question earlier as I found the solution – Tabbi Apr 02 '19 at 09:14

How to extract a list of SNPs from summary data according to p-value in R?

1 Answers1