Search found 4 matches

by shirleydaidai
Fri Apr 20, 2018 6:58 am
Forum: ProbABEL
Topic: Is paxoxph function suitable for small dataset?
Replies: 0
Views: 1516

Is paxoxph function suitable for small dataset?

Hello, I was trying to run pacoxph for a small dataset (e.g. N=30). But all the results were "nan". my code, for i in {1..22};do /media/epiroot/_1/home/Dai/ProbABEL-0.5.0/bin/pacoxph -p pheno.txt -d ../chr${i}/chr${i}_out.dose.fvi -i chr${i} --out coxres_chr${i} --map chr${i}.m...
by shirleydaidai
Wed Feb 22, 2017 9:22 am
Forum: GenABEL
Topic: impute2mach error
Replies: 21
Views: 12897

Re: impute2mach error

Hello, I came across the same error message after source "impute2databel.R". Is there some update info available? > library('GenABEL') Loading required package: MASS Loading required package: > library(DatABEL) DatABEL v.0.9-6 loaded > source("impute2databel.R") > im...
by shirleydaidai
Fri Feb 17, 2017 12:59 am
Forum: GenABEL
Topic: Imputation output filter queation
Replies: 0
Views: 408

Imputation output filter queation

Hi, I used "impute2databel" function, to generate *.fvi and *.fdv files from impute2 output. impute2databel("chr22.impute2", "chr22.phased.sample","out", makeprob=TRUE, old=FALSE) I wonder if GenABEL package has a function to filter info file or gen file by r2...
by shirleydaidai
Tue Feb 14, 2017 7:17 am
Forum: ProbABEL
Topic: p values extracted from pacoxph output
Replies: 1
Views: 3673

p values extracted from pacoxph output

Hello, I used pacoxph function to do survival analysis for my imputation data. The first few lines of "regression_add.out.txt": name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom beta_SNP_add sebeta_SNP_add chi2_SNP rs9628072 G A 0.095 1 1 1 220 0.0954545 22 -0.112741 0.289786 ...

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