VS.Hist: plot histplot for the return value of 'meta.TradPerm' and...

In MCPerm: A Monte Carlo permutation method for multiple test correlation

Description

plot histplot for the return value of 'meta.TradPerm' and 'meta.MCPerm' for certain study or meta analysis.

Usage

VS.Hist(Trad_data, MC_data, Trad_col = "grey", MC_col = "black", 
    title = NULL, xlab = NULL)

Arguments

Trad_data	the return value of function 'meta.TradPerm', e.g. 'perm_case_11' of certain stuy, 'perm_Qp', 'perm_p' etc.
MC_data	the return value of function 'meta.MCPerm', e.g. 'perm_case_11' of certain stuy, 'perm_Qp', 'perm_p' etc.
Trad_col	the color for the histplot body of 'Trad_data', default value is 'grey'.
MC_col	the color for the histplot border of 'MC_data', default value is 'black'.
title	the main title(on top).
xlab	X axis label.

Details

Plotting histplot for the return value(e.g. 'perm_case_11' of certain stuy, 'perm_Qp', 'perm_p' etc) of 'meta.TradPerm' and 'meta.MCPerm' is to compare the simulative data distribution got by TradPerm and MCPerm method whether are same.

MCPerm details see chisq.MCPerm. TradPerm details see chisq.TradPerm.

Author(s)

Lanying Zhang and Yongshuai Jiang <[e-mail]>

References

William S Noble(Nat Biotechnol.2009): How does multiple testing correction work?

Edgington. E.S.(1995): Randomization tests, 3rd ed.

See Also

meta.MCPerm, meta.TradPerm, chisq.MCPerm, chisq.TradPerm, VS.QQ, VS.CDC, VS.KS, VS.Allele.Hist, VS.Genotype.Hist, PermMeta.LnOR.Hist, PermMeta.Hist

Examples

## import data
# data(MetaGenotypeData)
## delete first line which contains the names of each column
# temp=MetaGenotypeData[-1,];
# rowNum=nrow(temp)
# gen=matrix(0,nrow=rowNum,ncol=1);
# aff=matrix(0,nrow=rowNum,ncol=1);
# for(j in 1:rowNum){
	 # gen[j,]=paste(temp[j,14],temp[j,15],sep=" ");
	 # case_num=length(unlist(strsplit(temp[j,14],split=" ")));
	 # control_num=length(unlist(strsplit(temp[j,15],split=" ")));
	 # case_aff=paste(rep(2,case_num),collapse=" ");
	 # control_aff=paste(rep(1,control_num),collapse=" ");
	 # aff[j,]=paste(case_aff,control_aff,sep=" ");
# }
# result1=meta.TradPerm(gen,aff,split=" ",sep="/",naString="-",
    # model="allele",method="MH",repeatNum=1000) 
# result1
## plot study 12
# Trad_case_1=2*result1$perm_case_11[12,]+result1$perm_case_12[12,]

## import data
# data(MetaGenotypeCount)
## delete the first line which is the names for columns.
# temp=MetaGenotypeCount[-1,,drop=FALSE]
# result=meta.MCPerm(case_11=as.numeric(temp[,14]),case_12=as.numeric(temp[,16]),
	 # case_22=as.numeric(temp[,18]),control_11=as.numeric(temp[,15]),
	 # control_12=as.numeric(temp[,17]),control_22=as.numeric(temp[,19]),
	 # model="allele",method="MH",repeatNum=100000)
# result2
## plot study 12
# MC_case_1=2*result2$perm_case_11[12,]+result2$perm_case_12[12,]

# VS.Hist(Trad_case_1,MC_case_1,title="Histplot for case_1")
# VS.Hist(result1$perm_Qp,result2$perm_Qp,title="Histplot for Qp")
# VS.Hist(result1$perm_p,result2$perm_p,title="Histplot for p")

MCPerm documentation built on May 29, 2017, 11:27 a.m.