html {GeneticsBase} | R Documentation

## Generate summary table files for genotype objects

### Description

Generate summary table files for genotype objects

### Usage

    #### HTML file format
    html
    ## S3 method for class 'LD':
    html(x, filename = "", digits = 3, ...)
    ## S3 method for class 'GeneticsBaseSummary':
    html(x, filename = "", ...)
    ## S3 method for class 'markerSummary':
    html(x, filename = "", plot.format = "pdf",
                       sep=".", verbose=TRUE, ...)

    #### plain text file format
    txt
    ## Default S3 method:
    txt(x, filename="", eol="\n", ...)
    ## S3 method for class 'markerSummary':
    txt(x, filename = "", plot.format = "pdf",
                       sep=".", verbose=TRUE, ...)

    #### LaTex file format
    latex
    ## Default S3 method:
    latex(x, filename="", ...)
    ## S3 method for class 'LD':
    latex(x, filename = "", digits = 3, ...)
    ## S3 method for class 'GeneticsBaseSummary':
    latex(x, filename = "", ...)
    ## S3 method for class 'markerSummary':
    latex(x, filename = "", plot.format = "pdf",
                       sep=".", verbose=TRUE, ...)

### Arguments

`x` | Object to be rendered to html/txt/latex
`filename` | Output filename, see below for details.
`eol` | End of line marker, defaults to `"\n"`. MS-DOS/MS-Windows uses `"\r\n"`
`digits` | Number of digits to display
`plot.format` | Graphics format for LD plot. Only `"pdf"` is currently supported
`sep` | Separatior used to join the file prefix provided by `filename` and descriptive text when generating file names
`verbose` | Show names of created files.
`...` | Additional parameters to pass to component methods

### Details

For `alleleSummary`, `genotypeSummary`, and `LD` objects, the `filename` argument is either the exact name of the file to be created, or "" which will print the output to the console.

For `markerSummary` objects, `filename` may be either `""` or a prefix used to create file names. If `filename=""` all output is printed to the R console. Otherwise, filenames for each component are constructed by combining the prefix specified by `filename`, the separator specified by `sep`, a string descibing the file contents (one of "alleleSummary", "genotypeSummary", and "LD"), and the file extension ".html".

### Value

Nothing of interest

### Author(s)

Nitin Jain nitin_jain@pfizer.com and Gregory R. Warnes warnes@bst.rochester.edu

### See Also

`alleleSummary`, `genotypeSummary`, `markerSummary`, `LD`

### Examples

    data(CAMP)

    ###
    # Generate a plain text allele summary table
    ###
    aS <- alleleSummary(CAMP)
    # display inline
    txt(aS, filename="")
    # create CAMP_alleleSummary.txt
    txt(aS, filename="CAMP.alleleSummary.html")

    ###
    # Generate an HTML genotype summary table
    ###
    gS <- genotypeSummary(CAMP)
    # display inline
    html(gS, filename="")
    # create CAMP_genotypeSummary.html
    html(gS, filename="CAMP.genotypeSummary.html")

    ###
    # Generate a LaTeX Linkage Disequilibrium table
    ###
    ld <- LD(CAMP)
    # display inline
    latex(ld, filename="")
    # create CAMP_LDSummary.html
    latex(ld, filename="CAMP.LD.html")

    ###
    # Generate a complete set of summary tables
    ###
    mS <- markerSummary(CAMP)
    # Plain text format
    txt(mS, filename="CAMP", sep="_")
    # HTML format
    html(mS, filename="CAMP", sep="_")
    # LaTeX format
    latex(mS, filename="CAMP", sep="_")

[Package GeneticsBase version 1.0.0 Index]