Confusion to the multiple base and target phenotypes

[xujiay...@gmail.com]

Hi,
Good night ! Here are the commands of multiple base and target phenotypes according to the mannual, Where is the invalid command?? It showed "ERROR: Please Supply a TARGET DATA SET" !!!


R -q --file=./PRSice_v1.25.R --args
multiple.base.phenotypes T
base PHEN.NAME.assoc.linear
base.phenotypes.names SSGAC_EduYears_Rietveld2013_publicrelease,SSGAC_College_Rietveld2013_publicrelease SSGAC_EduYears_Rietveld2013_publicrelease.assoc.linear SSGAC_College_Rietveld2013_publicrelease.assoc.linear
multiple.target.phenotypes T
target.phenotypes
pheno.file 1 ADNI1_Genotypes_Filt_CEU_final 2 ADNI1_Genotypes_Filt
target.phenotypes.binary T
slower 0.0001
supper 1
sinc 0.001
covary F
clump.snps T
plink ./plink_1.9_linux_160914
figname 1_SSGAC_EduYears_PRS

> library(batch)
> start.time <- proc.time()[3]
> options(echo = FALSE)
 #################################
 #
 #
 #
 #
 # PRSice: Polygenic Risk Score software
 #
 # Jack Euesden, Cathryn M. Lewis, Paul F. O'Reilly 2014
 #
 #
 # If you use PRSice in published work, please cite:
 #
 # "PRSice: Polygenic Risk Score software"
 # Euesden, Lewis, O'Reilly, Bioinformatics (2015) 31 (9):1466-1468
 #
 #
 #
 # 
 #################################
 #################################
 #
 #  Read in Command Line Arguments & interpret
 #
 #################################
$multiple.base.phenotypes
[1] "T"

$base
[1] "PHEN.NAME.assoc.linear"

$base.phenotypes.names
[1] "SSGAC_EduYears_Rietveld2013_publicrelease,SSGAC_College_Rietveld2013_publicrelease"

$SSGAC_EduYears_Rietveld2013_publicrelease.assoc.linear
[1] "SSGAC_College_Rietveld2013_publicrelease.assoc.linear"

$multiple.target.phenotypes
[1] "T"

$target.phenotypes
[1] "pheno.file"

$`1`
[1] "ADNI1_Genotypes_Filt_CEU_final"

$`2`
[1] "ADNI1_Genotypes_Filt"

$target.phenotypes.binary
[1] "T"

$slower
[1] 1e-04

$supper
[1] 1

$sinc
[1] 0.001

$covary
[1] "F"

$clump.snps
[1] "T"

$plink
[1] "./plink_1.9_linux_160914"

$figname
[1] "1_SSGAC_EduYears_PRS"

Using data on multiple phenotypes for target data
Constructing Polygenic Scores for  SSGAC_EduYears_Rietveld2013_publicrelease  Risk
 #################################
 #
 #  Check options match
 #
 #################################
[1] "ERROR: Please Supply a TARGET DATA SET"

[Joni Coleman]

You have not supplied a target file (i.e. a PLINK bed,bim,fam binary) containing the genotype data to run PRSice on. 

[xujiay...@gmail.com]

But the file named "ADNI1_Genotypes_Filt_CEU_final" and "ADNI1_Genotypes_Filt" are all the target data, which were plink binary format. I think the parts of Multiple phenotypes in manual were not clear for me. What't the command order of setting multiple target data ??

[Joni Coleman]

Your command to R is wrong. Spaces start new arguments, so you need to make sure you don't insert spaces accidentally. I've repeated your command below, with corrections in bold and comments (not to be run!) in italics. 

It looks as though you have two different targets, rather than a single target dataset with multiple phenotypes? If this is the case, you need to run PRSice twice (once for each target), rather than combining them in a single command.

Command (assuming two targets, rather than one target with two phenotypes)

R -q --file=./PRSice_v1.25.R --args
multiple.base.phenotypes T 
base PHEN.NAME.assoc.linear 

base.phenotypes.names SSGAC_EduYears_Rietveld2013_publicrelease,SSGAC_College_Rietveld2013_publicrelease [deleted SSGAC_EduYears_Rietveld2013_publicrelease.assoc.linear SSGAC_College_Rietveld2013_publicrelease.assoc.linear - these files are called by the combination of the base and base.phenotypes.names arguments]
target ADNI1_Genotypes_Filt_CEU_final 
[deleted multiple.target.phenotypes T, target.phenotypes, pheno.file 1 ADNI1_Genotypes_Filt_CEU_final 2 ADNI1_Genotypes_Filt, target.phenotypes.binary T - you have two target datasets, not one dataset with two phenotypes]  

[xujiay...@gmail.com]

Hi,
I have corrected the command as you suggested,however, another error

R -q --file=./PRSice_v1.25.R --args
multiple.base.phenotypes T
base PHEN.NAME.assoc.linear
base.phenotypes.names SSGAC_EduYears_Rietveld2013_publicrelease,SSGAC_College_Rietveld2013_publicrelease

target ADNI1_Genotypes_Filt_CEU_final

slower 0.0001
supper 1
sinc 0.001

covary T
user.covariate.file covarance.covary
clump.snps T
plink ./plink_1.9_linux_160914
figname SSGAC_PRS_covar

$target
[1] "ADNI1_Genotypes_Filt_CEU_final"

$slower
[1] 1e-04

$supper
[1] 1

$sinc
[1] 0.001

$covary

[1] "T"

$user.covariate.file
[1] "covarance.covary"

$clump.snps
[1] "T"

$plink
[1] "./plink_1.9_linux_160914"

$figname

[1] "SSGAC_PRS_covar"

Constructing Polygenic Scores for  SSGAC_EduYears_Rietveld2013_publicrelease  Risk
 #################################
 #
 #  Check options match
 #
 #################################

[1] "Using current directory as working directory"
 #################################
 #
 #  Check base input format
 #
 #################################
[1] "WARNING: No CHR column in base data"
[1] "WARNING: No BP column in base data"
[1] "NB: READING BETA NOT ODDS RATIO"
 #################################
 #
 #   Remove Ambiguous SNPs
 #
 #################################
 #################################
 #
 #   Clump
 #
 #################################
 #################################
 #
 #   Deal with strand flips if target is in genotype format and produce input files for polygenic scoring
 #
 #################################
 #################################
 #
 #   Polygenic scoring!
 #
 #################################
 #################################
 #
 #   Regression Models
 #
 #################################
Regression Models: 10% Complete
Regression Models: 20% Complete
Regression Models: 30% Complete
Regression Models: 40% Complete
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Regression Models: 70% Complete
Regression Models: 80% Complete
Regression Models: 90% Complete
Regression Models: 100% Complete
 #################################
 #
 #   High Density Plots
 #
 #################################
Saving 7 x 7 in image
 #################################
 #
 #   Barplots
 # Bars for inclusion can be changed using the barchart.levels option
 #################################
Saving 7 x 7 in image
Error in data.frame(top.thresh.pval) : object 'top.thresh.pval' not found
Execution halted