search

diazlab / CONICS

CONICS: COpy-Number analysis In single-Cell RNA-Sequencing
73 stars 28 forks source link

error when connecting to BioMart #2

Closed ysbioinfo closed 6 years ago

ysbioinfo commented 6 years ago

HI I got an error when I tried to run CONICs using the example data:

gene_pos=getGenePositions(rownames(suva_expr)) Request to BioMart web service failed. The BioMart web service you're accessing may be down. Check the following URL and see if this website is available: http://http://dec2016.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt Error in if (!grepl(x = registry, pattern = "^\n*")) { : argument is of length zero It seems like something goes wrong when I connect to BioMart. Do you have any advice on solving this problem? Many thanks!

diazlab commented 6 years ago

Hi Snoopy,

  1. great name
  2. did you try clicking the link to see if biomart was in fact down?

Sent from my Verizon 4G LTE Droid On May 18, 2018 7:34 PM, snoopy-448 notifications@github.com wrote:

HI I got an error when I tried to run CONICs using the example data:

gene_pos=getGenePositions(rownames(suva_expr)) Request to BioMart web service failed. The BioMart web service you're accessing may be down. Check the following URL and see if this website is available: http://http://dec2016.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt Error in if (!grepl(x = registry, pattern = "^\n*")) { : argument is of length zero It seems like something goes wrong when I connect to BioMart. Do you have any advice on solving this problem? Many thanks!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/diazlab/CONICS/issues/2, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHQSIQGYkG5qdYRhv56On7L9o8t2tYpbks5tz4SagaJpZM4UFiuD.

ysbioinfo commented 6 years ago

Thanks for your quick reply! I check that link and cannot open it. Maybe I have to wait until biomart works again. By the way , I am so happy that you like my name, haha

ysbioinfo commented 6 years ago

Hi, the connection to biomart is still failed for me. I'd appreciate if you could tell me the output format of getGenePositions so I can produce this table by myself. Such as, if I run gene_pos = getGenePositions(c('gene1', 'gene2')) what would be in the gene_pos then? Thank you !

soerenmueller commented 6 years ago

Hi snoopy - Thanks for using CONICS :) I just checked the getGenePosistions function and it works fine on windows and Unix, R 3.4.2. What version of R are you using? I remember a while ago biomart changed something in the underlying function, so if you have an outdated biomart package this might be the reason.

Either way, here is an output of the getGenePosistions function:

gene_pos[700:730,]
    ensembl_gene_id hgnc_symbol chromosome_name start_position end_position
477 ENSG00000188157        AGRN               1        1020123      1056118
479 ENSG00000135744         AGT               1      230702523    230714297
483 ENSG00000177674      AGTRAP               1       11736084     11754802
486 ENSG00000153207      AHCTF1               1      246839098    246931978
488 ENSG00000168710      AHCYL1               1      109984686    110023741
490 ENSG00000126705       AHDC1               1       27534035     27604431
501 ENSG00000186063        AIDA               1      222668013    222713210
514 ENSG00000176092       AIM1L               1       26321859     26354130
515 ENSG00000163568        AIM2               1      159062484    159147096
522 ENSG00000196581       AJAP1               1        4654732      4792534
525 ENSG00000004455         AK2               1       33007940     33080996
527 ENSG00000162433         AK4               1       65147549     65232145
528 ENSG00000154027         AK5               1       77282051     77559969
548 ENSG00000174574     AKIRIN1               1       38991223     39006059
551 ENSG00000162641      AKNAD1               1      108815898    108858228
552 ENSG00000117448      AKR1A1               1       45550543     45570049
563 ENSG00000053371      AKR7A2               1       19303965     19312146
566 ENSG00000162482      AKR7A3               1       19282558     19289250
567 ENSG00000211454       AKR7L               1       19265982     19274194
571 ENSG00000117020        AKT3               1      243488233    243851079
594 ENSG00000159423     ALDH4A1               1       18871430     18902781
599 ENSG00000143149     ALDH9A1               1      165662216    165698863
609 ENSG00000172339       ALG14               1       94974407     95072945
616 ENSG00000088035        ALG6               1       63367590     63438562
643 ENSG00000162551        ALPL               1       21509372     21578412
651 ENSG00000156150        ALX3               1      110059994    110070700
669 ENSG00000181754      AMIGO1               1      109504175    109509738
679 ENSG00000116748       AMPD1               1      114673090    114695618
680 ENSG00000116337       AMPD2               1      109616104    109632051
685 ENSG00000237763       AMY1A               1      103655290    103664554
686 ENSG00000174876       AMY1B               1      103687415    103696680
ysbioinfo commented 6 years ago

Thanks a lot!