Skip to content

Fix/ancestry formatter bug #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
glm4 wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Fix/ancestry formatter bug #5

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
b670f00
Merge pull request #2 from asiadmitchell/master
glm4 Mar 15, 2019
5ea5472
Fix Ancestry files formatter error
glm4 Mar 18, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion scripts/format_ancestry_com_as_23andme.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,9 @@ format_ancestry_com_as_23andme <- function(path) {
if(ncol(testRead)!=5) {
stop("testRead of file didn't have 5 columns (as it should have when invoking ancestry.com conversion)")
}

snpID <- list('rs','i','d')
if(unique(unique(sub("[0-9]+$","",testRead2[,1]))%!in%snpID)) {
if(unique(unique(sub("[0-9]+$","",testRead[,1]))%!in%snpID)) {
stop(safeError("testRead seemed like ancestry.com data, but didn't have rs IDs in column 1"))
}

Expand Down