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Last data update: 2014.03.03

R: Summary plot of the effect sizes and their correlations for a...

betas_plot

R Documentation

Summary plot of the effect sizes and their correlations for a SNP of interest

Description

betas_plot returns a pdf file containing information about the meta-analysis combined effect sizes (beta coefficients) for a chosen SNP of interest.

Usage

  betas_plot(SNP, res.file = NULL, data = NULL,
    trait.names = NULL, out.file = "Betas.pdf", col = NULL,
    orig.files = NULL, cohort.names = NULL)

Arguments

`SNP`	A SNP of interest, e.g. a SNP that is significantly associated to the analysed traits.
`res.file`	File name of the `multi_meta` results containing effect sizes for the above `SNP`. This is an alternative to `data`.
`data`	Object containing results from the `multi_meta` function and the above `SNP`. This is an alternative to `file`.
`trait.names`	Vector of analysed trait names to appear on the plot.
`out.file`	File name for the output plot.
`col`	Colours for the heat-map plot. Combinations of several colours are possible. If left blank a heat-map in scales of grey is produced.
`orig.files`	List of files with multivariate results for each cohort.
`cohort.names`	Names of the cohorts included in the meta-analysis.

Details

The plot produced can be a useful tool for visualizing effect sizes across all traits, and the correlation between them. The plot will have two panels:

effect sizes with 95% confidence interval for each trait;
a heat-map showing correlations between betas.

Two different types of input are allowed:

a data.frame, containing the output from the multi_meta function for at least the specified SNP. This is the best choice if results have already been loaded into the R workspace.
a file name containing the output from multi_meta for at least the specified SNP. The separator field is set to white space. This file can be a subset of the complete results file (suggested), e.g. a file containing only significant SNPs.

Value