User: zwang10

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zwang100
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Posts by zwang10

<prev • 23 results • page 1 of 3 • next >
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Comment: C: R: read.plink Error
... Thank you very much for your help.let me try. ...
written 2.3 years ago by zwang100
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Comment: C: R: read.plink Error
... I did not get any output. ...
written 2.3 years ago by zwang100
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R: read.plink Error
... Using `read.plink` from `snpMatrix` I use following command to read bed file in R: read.plink("/home/chr22_pos_16854001_to_16857000",na.strings = "-9") However, it shows Error in `row.names<-.data.frame`(`*tmp*`, value = value) : duplicate 'row.names' are not allowed In add ...
R bioconductor plink bed written 2.3 years ago by zwang100 • updated 2.3 years ago by chrchang5234.2k
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SOLVED: how to change SnpMatrix in to numeric
... I use `read.plink` from package `snpStats`. I use following to read `bed` file, and I want to get the 0,1,2 matrix. GENOTYPE=read.plink("chr22_1",na.strings = "NA") Then, from the [manuals][1], I know there is a "genotypes" value of `GNEOTYPE`, which is an object of class "SnpMatrix". And I got ...
R snpmatrix written 2.3 years ago by zwang100 • updated 9 months ago by catherinem.ross0
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R:Cannot install snpStats packages
... I follow the instruction from https://www.bioconductor.org/install/. But I got error as following > source("http://bioconductor.org/biocLite.R") Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 'lib = "/share/apps/R/3.1.1/intel/2013.0.028/lib64/R/library ...
R bioconductor written 2.3 years ago by zwang100 • updated 2.3 years ago by Guangchuang Yu2.0k
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R:how to read bed file with identical Famliy ID by read.plink
... I have three files, `chr_22.bed`,`chr_22.bim`,`chr_22.fam`. I always use `read.plink` from `MultiPhen` to get snp matrix in R genotype=read.plink(root="/home/chr_22") But today when I use the same command to get snp matrix, I got following error: Error in `row.names<-.data.frame`(`*tmp* ...
R plink bed file written 2.3 years ago by zwang100 • updated 18 months ago by ingrid.szilagyi0
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how to extract all genes from one chromosome simultaneously?
... Hello! I am using plink from https://www.cog-genomics.org/plink2/ I would like to extract all genes from chr1 to different gene files (each file is the data of one gene). I write a loop for --from-bp and --to-bp according to the pos of different gene. Each time I run command (for example) plin ...
plink written 2.6 years ago by zwang100 • updated 2.6 years ago by Rohit1.3k
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Can someone give me explanation about the output of plink
... I use following command to get 012 matrix plink --vcf test.vcf.gz --remove ID_of_miss_indv_for_plink --recode A --out TEST And then I get TEST.raw file. But I do not understand the meaning of column names for example rs62224609_C rs201290950_AAAACAAAC ._AACAAACAG ._AACAG ._ACAAG ._CAAAA ...
plink snp written 2.6 years ago by zwang100 • updated 2.6 years ago by Joey410
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Comment: C: vcftools: the length of each row is not same
... Sure. But my file is so large. The smallest file for chromsome is chr22 (about 4.1G). ...
written 2.6 years ago by zwang100
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Comment: C: vcftools: the length of each row is not same
... Do you have alternative tools to convert vcf.gz file into 012 matrix? ...
written 2.6 years ago by zwang100

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