histplot for the return value 'perm_LnOR' or 'perm_VARLnOR' of 'meta.MCPerm' or 'meta.TradPerm'

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Description

histplot for the return value 'perm_LnOR' or 'perm_VARLnOR' of 'meta.MCPerm' or 'meta.TradPerm'

Usage

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PermMeta.LnOR.Hist(PermMeta, plot = "LnOR", plot_study = "all", nrow = 2, ncol = 2, 
    main = "Background distribution for LnOR", title = NULL, 
	 xlab = "LnOR", hist_border_col = "black", arrows_col = "red", digits = 3)

Arguments

PermMeta

the result of function 'meta.TradPerm' or 'meta.MCPerm'.

plot

a character string indicating which return value of function 'meta.TradPerm' or 'meta.MCPerm' to be plot. The value can be "LnOR", "LnOR_VAR". "LnOR" and "LnOR_VAR" separetly plots the return value 'perm_LnOR' and 'perm_VARLnOR'. Default value is 'LnOR'.

plot_study

a numeric vector indicates which study(ies) in meta analysis to be plotted. Default value is 'all', which indicates all studies in meta analysis to be plotted.

nrow,ncol

positive integer, divides the device up into 'nrow' rows and 'ncol' columns. Default value is 2.

main

the main title (on top), default value is "Background distribution for LnOR".

title

the sub main title for each plotted study(on top).

xlab

X axis label, default value is 'LnOR'.

hist_border_col

the color for the border of histplot. Default value is 'black'.

arrows_col

the col of arrows which mark the place of the observed value. Default value is 'red'.

digits

integer indicating the number of decimal places. Default value is 3.

Details

Histplot for the return value('perm_LnOR','perm_VARLnOR') of 'meta.MCPerm' or 'meta.TradPerm'. And through arrows and legend to mark the observed value.

The symbol in the legend: 'LnOR' indicates the log odd ratio of observed value for the study. 'LnOR_VAR' indicates the variance of log odd ratio calculated by formule 1/ai+1/bi+1/ci+1/di (ai/bi/ci/di separetly are case/control two alleles count). 'sample' indicates the sample size of the study. 'mean' indicates the mean value of simulative log odd ratios. 'var' indicates the variance of simulative log odd ratios. 'p' is the percentage of more than the observed value.

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

Value

plot_study

the value of paramter 'plot_study'.

LnOR

the numeric vector of log odd ratio of the observed data for the plotted studies.

sample

the numeric vector of sample size of the plotted studies.

LnOR_VAR

the numeric vector of variance of the log odd ratio of obaserved value for the plotted studies.

VAR_LnOR

the numeric vector of variance of simulative log odd ratios for the plotted studies.

Author(s)

Lanying Zhang and Yongshuai Jiang <jiangyongshuai@gmail.com>

See Also

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

Examples

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## import data
# data(MetaGenotypeCount)
## delete first line
# temp=MetaGenotypeCount[-1,];
# 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",fixed_method="MH",random_method="DL",repeatNum=1000)
# PermMeta.LnOR.Hist(result,plot="LnOR",plot_study="all",nrow=2,ncol=2,
    # title=NULL,xlab="LnOR")
# PermMeta.LnOR.Hist(result,plot="LnOR_VAR",plot_study=c(3,5,12,21),nrow=2,ncol=2,
    # main="Background distribution for LnOR_VAR",title=NULL,xlab="LnOR_VAR")

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