User: GENOMIC_region

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Posts by GENOMIC_region

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GWAS: access Imputation probabilities: snpStats
... Hi there, I'm interested to work with .gen file generated from IMPUTE2 imputation tool. In particular I need probabilities per SNP. I use snpStats' function: test_impute<-read.impute("genotyped_snps_chr22.impute", rownames = NULL, nsnp = NULL, snpcol = 2) But the output I get is snpMatrix, wh ...
snpstats gwas imputation written 9 months ago by GENOMIC_region0
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Comment: C: IRanges which are not S4 generic: endoapply mendoapply error in loading oligocla
... Thank you for your reply. That helps; I'd to downgrade certain packages that were too new for Bioconductor version '3.6'.  ...
written 10 months ago by GENOMIC_region0
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IRanges which are not S4 generic: endoapply mendoapply error in loading oligoclasses
... I'm having issues for loading libraries: Step1: library("oligo",lib.loc="~/R_LIB") library("pd.huex.1.0.st.v2",lib.loc="~/R_LIB") Error: Loading required package: IRanges Error: package or namespace load failed for ‘IRanges’:  Functions found when exporting methods from the namespace ‘IRanges’ ...
oligoclasses iranges biocgenerics written 10 months ago by GENOMIC_region0
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... Thank you so so much for digging into this. :) ...
written 11 months ago by GENOMIC_region0
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Comment: C: GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... Thank you for your reply.    Yes, it works with larger sample size. Kinship I had with ten individuals had all negative values.  ...
written 11 months ago by GENOMIC_region0
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GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
... Hello, I'm using a small data of 10 people to work with GENESIS and generate relatedness using PC-relate function. I generate .gds file, create kinship using KING. When generating principal components I get error  Error in acc(object, NL[cnode]) : unmatched node provided   R 3.4.2 ############### ...
genesis pcair written 11 months ago by GENOMIC_region0
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Comment: C: Preprocessing of Human Gene 2.0 ST microarrays with oligo R package and annotati
... Hi James:    I get error:  could not find function "annotateEset" ...
written 12 months ago by GENOMIC_region0
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Comment: C: reading ped error when using the snpStats library
... Can you paste snpStats' version you're using? ...
written 15 months ago by GENOMIC_region0
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status was 'Couldn't connect to server': bioClite
... Hello, I'm using R's developer version. I need developer version of a library and hence R's unstable release.  So, I download latest R developer version, compile it on local directory.    > sessionInfo() R Under development (unstable) (2018-01-08 r74099) Platform: x86_64-pc-linux-gnu (64-bit) ...
bioclite written 15 months ago by GENOMIC_region0 • updated 15 months ago by Martin Morgan ♦♦ 23k
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Error in snpStats::read.pedfile: GeneGeneInter
... Hello all, I'm using genegeneinter package for epistasis analysis. I head into below error while creating initial data object: Error in snpStats::read.pedfile(file = file, ...) : No unambiguous snp names found on file In addition: Warning message: In if (length(line) == 0) break : closing unused ...
snpmatrix ped written 15 months ago by GENOMIC_region0

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