html {GeneticsBase} | R Documentation |
Generate summary table files for genotype objects
#### 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, ...)
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 |
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".
Nothing of interest
Nitin Jain nitin_jain@pfizer.com and Gregory R. Warnes warnes@bst.rochester.edu
alleleSummary
,
genotypeSummary
,
markerSummary
,
LD
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="_")