Error In Convert Snp Illumina
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FAQ Login Register Board index GenABEL Search [SOLVED] convert.snp.illumina error Questions about GenABEL (aka *ABEL) suite of packages Forum rules Please remember not to post any sensitive data on this public forum.The first few posts of newly registered users will be affymetrix snp moderated in order to filter out any spammers.When get a solution to the problem luminex snp you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier sequenom snp for the community to follow the posts yet to be attended. Post Reply Print view Search Advanced search 4 posts • Page 1 of 1 plantgirl Posts: 2 Joined: Thu Sep 04, 2014 4:17 pm [SOLVED]
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convert.snp.illumina error Quote Postby plantgirl » Thu Sep 04, 2014 4:24 pm Hello,I would like to use GenABEL only to use the check.marker functions. I have two questions.First, am I required to import phenotype data if I only want to check my genotypes?Second, when I try to import my data, I receive the following error message:> head(test[,1:10]) name chr pos V029 V035 V047 V030 V042 V036 V0481 m5 1 13829072 AA AA plink2 AA AA AA AA AA2 m16 1 14022289 GG GG GG GG GG GG GG3 m18 1 1230878 CC CC CC CC CC CC CC4 m20 5 16450602 AA 00 AA 00 00 00 AA5 m21 1 14161828 CC CC CC CC CC CC CC6 m28 1 14224986 AA AA AA AA AA AA AA> convert.snp.illumina(inf="test.csv",out="gen.raw", strand="u")Reading genotypes from file 'test.csv' ...Error in convert.snp.illumina(inf = "test.csv", out = "gen.raw", strand = "u") : First three fields are missing in line 2!Thank you for your time! Last edited by plantgirl on Fri Sep 05, 2014 12:42 pm, edited 1 time in total. Top lckarssen Site Admin Posts: 303 Joined: Tue Jan 04, 2011 3:04 pm Location: Utrecht, The Netherlands Re: convert.snp.illumina error Quote Postby lckarssen » Fri Sep 05, 2014 9:54 am plantgirl wrote:First, am I required to import phenotype data if I only want to check my genotypes?Yes, I think so. Baisc phenotypic information is an integral part of a GenABEL R object (i.e. an object of gwaa.data class). Please see appendix A in the GenABEL tutorial (PDF) for more information if you haven't already done so. Note that sex information is used, for example in the check.marker() function.plantgirl wrote:Second, when I try to import my data, I receive the following error message:Code: Se
annoying error after the import of PLINK data format R blog By Andrea Pedretti July 12, 2012 Tags: bioR, GenABEL No Comments In the previous post we saw how much convenient could be GenABEL in the management of genotypic/phenotypic data. We introduced the import of genotypic data from an Illumina format file: > convert.snp.illumina(inf = "gen.illu", out = "gen.raw", strand = "file") but what happens if you're analysing your data with PLINK, the open source toolset for GWAS? GenABEL provides an useful function: > convert.snp.tped(tped = "dataset.tped", tfam="dataset.tfam", out = "gen.raw", strand = "+")
http://forum.genabel.org/viewtopic.php?t=892 /> This function allows you to import the transposed-ped format file and the tfam format file and it permits to convert them into the .raw file which contains the genotypic raw data readable by load.gwaa.data function. The conversion is performed by C++ code that is both fast and memory efficient. It's all great. But.. when you use the function: > df <- load.gwaa.data(phe = phe.txt", gen http://www.milanor.net/blog/genabel-an-annoying-error-after-the-import-of-plink-data-format/ = "gen.raw") you could receive this warning: person with id = a123456 was not found in genotypic file; excluded Good! In your phenotypic dataset there are more person than in the genotypic dataset, GenABEL understands that 'mistake' and it doesn't load that person. What happens you are adding a person who is present in the genotypic file and not in the phenotypic file? person with id = 654321a was not found in phenotypic file!!! - FATAL Bad. You'll get an error! So you need to fix your dataset: you have to delete persons, which aren't present in phenotypic data, from your genotypic dataset. This kind of problem could happen when you receive the datasets from another person (it's my case). You could edit the .tfam o .tped files. You should check the persons present in your phenotypic file, then you have to take off the rows in the .tfam file corresponding to those persons and the corresponding columns in the .tped file. There could be another solution: > convert.snp.tped(tped = "genabelGWASALL.tped", tfam="genabelGWASALL.tfam", out = "genot.raw", strand = "+")
> file_tfam <- read.table(file="genabelGWASALL.tfam", sep=' ', head=FALSE) # genotypes
> file_phe <- read.table(file="phe.txt", sep=' ', head=TR
faq • rss Community Log In Sign Up Add New Post Question: Illumina genotyping report to Plink files 0 19 months ago by egustavsson • 0 Canada egustavsson • 0 wrote: I just received my genotyping report files from Illumina, with the locus summary file, and I want to convert the files to Plink files. https://www.biostars.org/p/135156/ They came as CSV so I converted them to tab delimited (.txt) and wanted to use gcta to http://svitsrv25.epfl.ch/R-doc/library/GenABEL/html/convert.snp.illumina.html convert into map + ped. However, I get the map file but get an error ("segmentation error") when it tries to create the .ped My locus summary file Index Name Chr Position AA Freq AB Freq BB Freq Call Freq Minor Freq 10% GC 50% GC 1 1:10002775-GA 1 10002775 0.00 error in 0.00 1 1 0.00 0.4114687 0.4114687 2 1:100152282-CT 1 100152282 0.00 0.00 1 1 0.00 0.3868383 0.3868383 3 1:100154376-GA 1 100154376 0.00 0.00 1 1 0.00 0.4968892 0.4968892 4 1:100154844-CA 1 100154844 error in convert 0.00 0.00 1 1 0.00 0.3769583 0.3769583 Genotyping report file [Header] GSGT Version 1.9.4 Processing Date 3/12/2015 2:17 PM Content MEGA_Consortium_15063755_B1.bpm Num SNPs 1548495 Total SNPs 1705969 Num Samples 572 Total Samples 576 File 1 of 6 [Data] SNP Name Sample ID Allele1 - Forward Allele2 - Forward GC Score X Y 1:10002775-GA WG0238334-DNAA01_Control G G 0.4115 0.027 1.531 1:100152282-CT WG0238334-DNAA01_Control C C 0.3868 0.072 1.651 1:100154376-GA WG0238334-DNAA01_Control G G 0.4969 0.019 0.855 Is there any way of doing this? I would appreciate any suggestions. Thank you. conversion plink snp illumina • 1.1k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 19 months ago • written 19 months ago by egustavsson • 0 1 Try this Converting Illumina Raw Genotype Data Into Plink Ped Format Formatting Beadstudio Final Report Into Plink ADD REPLY • link written 19 months ago by Jimbou • 510 0 19 months ago by egustavsson • 0 Canada egustavsson • 0 wrote: Thanks! I had to create the .lgen by moving some rows from the initial report and then Plink worked fine for creating the .ped ADD COMME
Usage convert.snp.illumina(infile, outfile, strand = "+", bcast = 10000000) Arguments infile Pre-makeped linkage genotypic data file name outfile Output data file strand Specification of strand, one of "u" (unknown), "+", "-" or "file". In the latter case, extra column specifying the strand (again, one of "u", "+", or "-") should be included on the infile. bcast Reports progress after reading bcast portion of SNP genotypes Details Input file is the one which could be typically obtained from Illumina BeadStudio software. For example: Name Chr Pos id1 id2 id3 rs1001 2 12897 AC AA AA rs2401 3 12357 AG GG AG rs123 3 5327 TC TT CC Here, every row corresponds to a SNP, and each column, starting with the 4th, corresponds to a person. When strand information is available (option strand="file"), the file should look like Accepted allele codes: 1/2, A/B, A/T, A/G, A/C, T/G, T/C, G/C, A/-, T/-, G/-, C/-. Here, "-" stands of a deletion. Missing data can be coded as "–" or "00". Make sure that the coding for missing is "00" if you use one of the codings A/-, T/-, G/-, C/-! Name Chr Pos Strand id1 id2 id3 rs1001 2 12897 + AC AA AA rs2401 3 12357 - AG GG AG rs123 3 5327 + TC TT CC Accepted strand coding: +, -, u (unknown) The procedure always codes genotypes that "0", "1" and "2" correspond to AA, AB, and BB, where B is the less frequent allele. Thus GWA analysis procedures will return effect of the minor allele. Value Does not return any value, but writes file with GenABEL raw data Note The function does not check if "outfile" already exists, thus it is always over-written Author(s) Yurii Aulchenko See Also load.gwaa.data, convert.snp.text, convert.snp.mach, convert.snp.tped Examples # # convert.snp.illumina(infile="pedin.18",out="genos.raw",strand="+") #