search

bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
64 stars 42 forks source link

importFromTable #27

Closed GracielaCaruso closed 4 years ago

GracielaCaruso commented 4 years ago

Hello! I am trying to use the QTLsegr package, but I have trouble with the ImportFromTable function. I have my data in comma delimited file (csv). The head is:

CHROM | POS | id | REF | ALT | AD_REF.LV | AD_ALT.LV | AD_REF.CV | AD_ALT.CV Chr01 | 22492233 | 1122 | G | A | 9 | 5 | 8 | 4 Chr01 | 22492228 | 1141 | G | A | 10 | 6 | 11 | 3 Chr01 | 22492206 | 1393 | G | A | 11 | 5 | 9 | 3 Chr01 | 22492264 | 1429 | C | T | 11 | 5 | 10 | 3

When I run the function, I get this message: "Error in importFromTable(file = "slSHQTLseqr.csv", highBulk = "HighBulk", : No 'CHROM' coloumn found. Además: Warning message: The following named parsers don't match the column names: CHROM, POS "

I will be very grateful if you can help me solve the problem!

Thanks in advance!

Graciela Caruso

bmansfeld commented 4 years ago

Graciela thanks for opening the issue. Before anything else, and just as a check, when you pasted the head of the csv were the | added by you manually? If they are in the actually csv then this is the problem. Let me know, Ben

GracielaCaruso commented 4 years ago

Ben, thanks for your attention. I copied the first rows of Excel. The symbol was added when I pasted the header here. The csv file has not the symbol ( | ). Graciela

bmansfeld commented 4 years ago

ok good! just checking.. do you mind sending me the top 100 rows of your csv? I can check what is breaking the import function.

GracielaCaruso commented 4 years ago

Excuse me for my incorrect English! I send you the file

El mar., 21 ene. 2020 a las 18:48, Ben Mansfeld (notifications@github.com) escribió:

ok good! just checking.. do you mind sending me the top 100 rows of your csv? I can check what is breaking the import function.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bmansfeld/QTLseqr/issues/27?email_source=notifications&email_token=ALXVC25JMPIRXP427EQ6A6DQ65UTBA5CNFSM4KIOCOY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJRMKUQ#issuecomment-576898386, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALXVC262EDSMAQQFUOYA7Y3Q65UTBANCNFSM4KIOCOYQ .

bmansfeld commented 4 years ago

No need to apologize! My Spanish is a lot worse!!!

bmansfeld commented 4 years ago

Hi I never received the file from you. You could upload a link here or email me. bmansfeld [at] danforthcenter.org

GracielaCaruso commented 4 years ago

Hi Ben I send you the file again

Thanks you

Graciela

---------- Forwarded message --------- De: Graciela Caruso gbcaruso67@gmail.com Date: mar., 21 ene. 2020 a las 19:13 Subject: Re: [bmansfeld/QTLseqr] importFromTable (#27) To: bmansfeld/QTLseqr < reply@reply.github.com>

Excuse me for my incorrect English! I send you the file

El mar., 21 ene. 2020 a las 18:48, Ben Mansfeld (notifications@github.com) escribió:

ok good! just checking.. do you mind sending me the top 100 rows of your csv? I can check what is breaking the import function.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bmansfeld/QTLseqr/issues/27?email_source=notifications&email_token=ALXVC25JMPIRXP427EQ6A6DQ65UTBA5CNFSM4KIOCOY2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJRMKUQ#issuecomment-576898386, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALXVC262EDSMAQQFUOYA7Y3Q65UTBANCNFSM4KIOCOYQ .