Example Outputs

Manhattan++ provides different ways in which individual cells can be labelled with information.

Types of reporting

1. Default Output (Reports configuration data)
2. Reporting known lead variants gene name
3. Reporting known lead variants rsids

Default

Labels cells with configuration file, report field set to TRUE, enabled by default

manhplusplot(infile = infile,outfile = "test", configfile = configfile, 
             snpfile = snpfile)

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Genes

The gene names of known reported peak SNPs (novel set to FALSE) from the snplist file displayed on plot, enabled with showgenes flag set to TRUE. This overrides reporting of individual cells specified in the config file. Novel variants are displayed in the table.

manhplusplot(infile = infile,outfile = "test", configfile = configfile, 
             snpfile = snpfile, showgenes = TRUE)

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RSIDs

The SNP IDs of known reported peak SNPs (novel set to FALSE) from the snplist file displayed on plot, enabled with showgenes flag set to TRUE and showrsids set to TRUE. This overrides reporting of individual cells specified in the config file. Novel variants are displayed in the table.

manhplusplot(infile = infile,outfile = "test", configfile = configfile, 
             snpfile = snpfile, showgenes = TRUE, showrsids = TRUE)

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