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 1.6.0 Index]