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Last data update: 2014.03.03

R: meta

meta	R Documentation

meta

Description

Perform the single-marker meta-analysis.

Usage

  meta(summary.files, lambda = NULL, sel.snps = NULL, only.meta = TRUE)

Arguments

`summary.files`	a character vector of file names containing the summary results of SNPs included in one or multiple studies. Each file must be able to be read by `read.table`. Each file must have columns called "SNP", "RefAllele", "EffectAllele", "BETA", and at least one of "SE", "P".
`lambda`	a numeric vector of inflation factors. Each file in `summary.files` should have one inflation factor specified in `lambda`. `NULL` if inflation is not adjusted.
`sel.snps`	a character vector of SNPs to be used in meta-analysis. The default is `NULL`, i.e., all SNPs are used.
`only.meta`	`TRUE` if do not returned individual summary data. The default is `TRUE`.

Details

The inverse-variance method is used by assuming a fixed effect model. The standard error is rescaled by sqrt{lambda}.

Value

meta returns a list containing

`meta.stat`	a data frame of summary statistics from meta-analysis. The summary statistics of individual studies specified in `summary.files` are also returned in the data frame if `only.meta` is `FALSE`. The standard error of individual studies are rescaled by `sqrt{lambda}`.
`conf.snps`	a character vector of SNPs with conflictive allele information.

Examples


study1 <- system.file("extdata", package = "ARTP2", "study1.txt.gz")
study2 <- system.file("extdata", package = "ARTP2", "study2.txt.gz")
snps <- c('rs13266821', 'rs4824130', 'rs1792438', 'rs1000047', 
          'rs1000017', 'rs6066771', 'rs12508128')

m1 <- meta(summary.files = c(study1, study2), lambda = c(1.10, 1.08), 
           sel.snps = snps)
m2 <- meta(summary.files = c(study1, study2), lambda = c(1.10, 1.08), 
           sel.snps = snps, only.meta = FALSE)

m1$conf.snps

m1$meta.stat
m2$meta.stat

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(ARTP2)
Loading required package: Formula
Loading required package: data.table
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ARTP2/meta.Rd_%03d_medium.png", width=480, height=480)
> ### Name: meta
> ### Title: meta
> ### Aliases: meta
> 
> ### ** Examples
> 
> 
> study1 <- system.file("extdata", package = "ARTP2", "study1.txt.gz")
> study2 <- system.file("extdata", package = "ARTP2", "study2.txt.gz")
> snps <- c('rs13266821', 'rs4824130', 'rs1792438', 'rs1000047', 
+           'rs1000017', 'rs6066771', 'rs12508128')
> 
> m1 <- meta(summary.files = c(study1, study2), lambda = c(1.10, 1.08), 
+            sel.snps = snps)
Loading summary files: Mon Jul  4 14:13:45 2016
Extracting allele information: Mon Jul  4 14:13:46 2016
Extracting SNPs with conflictive alleles: Mon Jul  4 14:13:46 2016
Merging summary statistics: Mon Jul  4 14:13:46 2016
Warning messages:
1: In read.table(summary.files[i], header = TRUE, as.is = TRUE, colClasses = col.class) :
  not all columns named in 'colClasses' exist
2: In load.summary.files(summary.files, lambda, sel.snps) :
  Direction is absent in /home/ddbj/local/lib64/R/library/ARTP2/extdata/study2.txt.gz. Function meta() assumed equal sample sizes for all SNPs in that study. Invalidation of this assumption can lead to false positive if summary data of this study is used in pathway analysis
> m2 <- meta(summary.files = c(study1, study2), lambda = c(1.10, 1.08), 
+            sel.snps = snps, only.meta = FALSE)
Loading summary files: Mon Jul  4 14:13:46 2016
Extracting allele information: Mon Jul  4 14:13:46 2016
Extracting SNPs with conflictive alleles: Mon Jul  4 14:13:46 2016
Merging summary statistics: Mon Jul  4 14:13:46 2016
Warning messages:
1: In read.table(summary.files[i], header = TRUE, as.is = TRUE, colClasses = col.class) :
  not all columns named in 'colClasses' exist
2: In load.summary.files(summary.files, lambda, sel.snps) :
  Direction is absent in /home/ddbj/local/lib64/R/library/ARTP2/extdata/study2.txt.gz. Function meta() assumed equal sample sizes for all SNPs in that study. Invalidation of this assumption can lead to false positive if summary data of this study is used in pathway analysis
> 
> m1$conf.snps
[1] "rs1792438"
> 
> m1$meta.stat
         SNP RefAllele EffectAllele         BETA         SE            P
1 rs12508128         T            A -0.057648934 0.01724617 0.0008296448
2  rs6066771         G            A  0.019109072 0.01686097 0.2570749913
3 rs13266821         C            T  0.028183212 0.02929865 0.3360853990
4  rs4824130         C            A  0.009487268 0.01351475 0.4826830106
5  rs1000047         T            C  0.010232406 0.02023773 0.6131302674
6  rs1000017         C            A -0.002891776 0.01914442 0.8799357941
  Direction
1       +?-
2       +?+
3       +??
4       ++?
5       ??+
6       ??-
> m2$meta.stat
         SNP RefAllele EffectAllele         BETA         SE            P
1 rs12508128         T            A -0.057648934 0.01724617 0.0008296448
2  rs6066771         G            A  0.019109072 0.01686097 0.2570749913
3 rs13266821         C            T  0.028183212 0.02929865 0.3360853990
4  rs4824130         C            A  0.009487268 0.01351475 0.4826830106
5  rs1000047         T            C  0.010232406 0.02023773 0.6131302674
6  rs1000017         C            A -0.002891776 0.01914442 0.8799357941
  Direction RefAllele.Study.1 EffectAllele.Study.1 BETA.Study.1 SE.Study.1
1       +?-                 A                    T  0.046519596 0.02466272
2       +?+                 G                    A  0.037395483 0.02573846
3       +??                 C                    T  0.028183212 0.02929865
4       ++?                 C                    A  0.009487268 0.01351475
5       ??+              <NA>                 <NA>           NA         NA
6       ??-              <NA>                 <NA>           NA         NA
   P.Study.1 Direction.Study.1 RefAllele.Study.2 EffectAllele.Study.2
1 0.05926376                +?                 T                    A
2 0.14625073                +?                 G                    A
3 0.33608540                +?              <NA>                 <NA>
4 0.48268301                ++              <NA>                 <NA>
5         NA              <NA>                 T                    C
6         NA              <NA>                 C                    A
  BETA.Study.2 SE.Study.2   P.Study.2 Direction.Study.2
1 -0.068298854 0.02412567 0.004640828                 -
2  0.005362335 0.02231609 0.810105393                 +
3           NA         NA          NA              <NA>
4           NA         NA          NA              <NA>
5  0.010232406 0.02023773 0.613130267                 +
6 -0.002891776 0.01914442 0.879935794                 -
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>