Description Usage Arguments Details Author(s) See Also Examples
View source: R/PermMeta.boxplot.R
boxplot for the result of 'meta.MCPerm' or 'meta.TradPerm'
1 2 3 | PermMeta.boxplot(PermMeta, plot = "Qp", true_data_pch = 3, pch_col = "red",
border_col = "red", fill_col = NULL,
main = "boxplot for heterogeneity Q p_vlaue", digits = 3)
|
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 "Qp"(default), "I2", "merged_LnOR", "merged_LnOR_VAR" or "merged_LnOR_p". And the value must be simulation data. 'Qp', "I2", "merged_LnOR", "merged_LnOR_VAR" and "merged_LnOR_p" separetly plots the return value 'perm_Qp', 'perm_I2', 'perm_merged_LnOR', 'perm_merged_VARLnOR', 'perm_merged_p'. |
true_data_pch |
the pch(default 3) to mark the observed value in the boxplot of simulation data. |
pch_col |
the color(default 'red') of pch. |
border_col |
the color(default 'red') for the border of boxplot. |
fill_col |
the filled color(default NULL) for the body of boxplot. |
main |
the main title (on top), default value is "boxplot for heterogeneity Q p_vlaue". |
digits |
integer(default 3) indicating the number of decimal places. See details. |
boxplot for the return value('perm_Qp','perm_I2','perm_merged_LnOR','perm_merged_VARLnOR', 'perm_merged_p') of 'meta.MCPerm' or 'meta.TradPerm'. And through 'pch' and text to mark the observed value.
The symbols in the legend: 'Q_stat' is the Q statistic for meta data heterogeneity; 'Q_p' is the p value of Q value(chi square distribution,the number of studies in meta analysis minus one is degree of freedom of Q value.); 'p.corrected' is the corrected p value by permutation; 'I2_stat' is the statistic I2(calculated by formula max(Q-d.f./Q, 0)) for meta data heterogeneity; 'merged_LnOR' is the merged log odd ratio of observed data; 'merged_LnOR_VAR' is the variance of log odd ratio for observed data; 'merged_LnOR_p' is the p value of log odd ratio of observed data which obey normal distribution.
MCPerm details see chisq.MCPerm
.
TradPerm details see chisq.TradPerm
.
Lanying Zhang and Yongshuai Jiang <jiangyongshuai@gmail.com>
meta.MCPerm
,
meta.TradPerm
,
chisq.MCPerm
,
chisq.TradPerm
,
VS.Hist
,
VS.KS
,
VS.Genotype.Hist
,
VS.Allele.Hist
,
PermMeta.LnOR.Hist
,
PermMeta.LnOR.CDC
,
PermMeta.LnOR.boxplot
,
PermMeta.LnOR.qqnorm
,
PermMeta.Hist
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ## 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)
## set working directory to save the plots.
# setwd("D:\")
# pdf("PermMeta.boxplot.pdf",height=6,width=6)
# PermMeta.boxplot(result,plot="Qp",
# true_data_pch=5,pch_col='red',border_col='black',fill_col=NULL,
# main="boxplot for heterogeneity Q p_vlaue")
# PermMeta.boxplot(result,plot="I2",
# true_data_pch=5,pch_col="red",border_col='black',fill_col=NULL,
# main="boxplot plot for heterogeneity I2")
# PermMeta.boxplot(result,plot="merged_LnOR",
# true_data_pch=5,pch_col="red",border_col='black',fill_col=NULL,
# main="boxplot plot for merged_LnOR")
# PermMeta.boxplot(result,plot="merged_LnOR_VAR",
# true_data_pch=5,pch_col="red",border_col='black',fill_col=NULL,
# main="boxplot plot for merged_LnOR_VAR")
# PermMeta.boxplot(result,plot="merged_LnOR_p",
# true_data_pch=5,pch_col="red",border_col='black',fill_col=NULL,
# main="boxplot plot for merged_LnOR_p")
# dev.off()
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