User: brianscomer

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Posts by brianscomer

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Comment: C: Split individual SNP genotypes into two columns per call in R when there are 2.4
... My matrix snpmatrix_df[1:3, 1:20] (note: row names and column names are included in this output but will not be in final ped file): family_id individual_id paternal_id maternal_id sex phenotype kgp5400438 kgp5400470 kgp5400471 xxxx_001 "IID" "xxxx_001" "0" "0 ...
written 2.9 years ago by brianscomer0
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Split individual SNP genotypes into two columns per call in R when there are 2.44 million columns
... Hi everyone: I am attempting to convert my snp matrix into a .ped file for use with Plink. I have successfully added all of the required information columns and just need to split all of my SNP columns which are currently in the following format ("AA") into two separate columns per SNP ("A" "A"). ...
R plink snp written 2.9 years ago by brianscomer0 • updated 2.9 years ago by Michael Dondrup45k
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Comment: C: Unable to manually create smlSet using manually created snpmatrix
... Thanks: The following code corrected the issue. eqtl_smlset<-make_smlSet(esetforeqtl, list(all=snpmatrix), organism="Homo sapiens", harmonizeSamples=TRUE) It will take a few hours to run the eQTL analysis in R before I will have confirmation that the manually constructed smlset works downs ...
written 2.9 years ago by brianscomer0
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Unable to manually create smlSet using manually created snpmatrix
... Hi I am attempting to create an smlSet for use in GGtools for eQTL analysis using a snpmatrix that was manually created using the following code: library(snpStats) snpmatrix<-new("SnpMatrix", snpmatrix) The original snpmatrix is simply a matrix object. I call the SnpMatrix object, I g ...
snpstats ggtools smlset snp snpmatrix written 2.9 years ago by brianscomer0 • updated 2.9 years ago by Vince Carey70
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Answer: A: Covariate remove from Expressionset using SVA to yield transformed_expressionset
... Actually, I found the answer to my question in another post: https://www.biostars.org/p/121489/ ...
written 2.9 years ago by brianscomer0
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Covariate remove from Expressionset using SVA to yield transformed_expressionset
... This may be a naive question but I am fairly new to bioinformatics and R in general. I need to perform eQTL analysis using GGtools and I am attempting to make a smlSet (genotype matrix + expressionset) using functions in GGtools. Is there a way I can correct my expressionset using SVA to generate ...
sva ggtools limma expressionset eqtl written 2.9 years ago by brianscomer0
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Comment: C: Bioconductor Package for import and analysis of Illumina HumanOmni2.5-4v1_c?
... Thanks. I actually already tried it but was told in a warning that the package was not compatible with my platform. I think the built-in annotations do not cover this version but they covered an earlier annotation version (I don't remember which at the moment but it might have been 2.5-4v1_b) of t ...
written 3.0 years ago by brianscomer0
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Bioconductor Package for import and analysis of Illumina HumanOmni2.5-4v1_c?
... Hi All: I am fairly new to bioinformatics and just obtained a dataset generated by the Illumina HumanOmni2.5-4v1_C platform. I need to determine if there is a package that will allow me to import and annotate the raw data starting from the idat files. I have the annotation files from ilumina but ...
R snp written 3.0 years ago by brianscomer0 • updated 3.0 years ago by andrew.j.skelton735.5k

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Scholar 2.9 years ago, created an answer that has been accepted. For A: Covariate remove from Expressionset using SVA to yield transformed_expressionset

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