getFullHtmlSpeCondResult {SpeCond} | R Documentation |
getFullHtmlSpeCondResult
generates a full result html page.
getFullHtmlSpeCondResult(SpeCondResult=NULL, L.specific.result = NULL, param.detection = NULL, page.name = "SpeCond_result", page.title = "Condition-specific analysis results", prefix.file = NULL, outdir="General_Result", sort.condition = "all", gene.page.info=NULL, heatmap.profile = TRUE, heatmap.expression = FALSE, heatmap.unique.profile = FALSE, expressionMatrix = NULL)
SpeCondResult |
the |
L.specific.result |
List of results present in the |
param.detection |
The parameter matrix used by the SpeCond detection procedure |
page.name |
The name of the result html page. The default is "SpeCond\_result" |
page.title |
The title of the result html page. The default is "Condition-specific analysis results" |
prefix.file |
a prefix added to the generated file(s) and the |
outdir |
the name of the directory in which the generated files will be created. The default is "General_result" |
sort.condition |
If the condition must sorted in the barplot presented the number of specific genes by condition. Can table the values: positive", "negative", "all": the conditions are sorted respectively by the number of specific genes detected as up-regulated, down-regulated or both |
gene.page.info |
the result of the |
heatmap.profile |
TRUE/FALSE, to print or not a heatmap showing the specific profile of the genes. The default is FALSE |
heatmap.expression |
TRUE/FALSE, to print or not a heatmap showing the expression of the genes. The default is FALSE |
heatmap.unique.profile |
TRUE/FALSE, to print or not a heatmap showing the unique specific profile. The default is FALSE |
expressionMatrix |
Must not be NULL if heatmap.expression=TRUE, must be the same as the input expression matrix. The default is NULL |
Either SpeCondResult
or L.specific.result
can be specified to use this function. If you use L.specific.result
you ahve tp define prefix.file
.
Florence Cavalli, florence@ebi.ac.uk
getGeneHtmlPage
library(SpeCond) data(expressionSpeCondExample) ##Perform the condition specific detection analysis with SpeCond() generalResult=SpeCond(expressionSpeCondExample, param.detection=NULL, multitest.correction.method="BY", prefix.file="E", print.hist.pv=TRUE, fit1=NULL, fit2=NULL, specificOutlierStep1=NULL) specificResult=generalResult$specificResult ##Produce the general html page results getFullHtmlSpeCondResult(SpeCondResult=generalResult, param.detection= specificResult$param.detection, page.name="Example_SpeCond_results", page.title="Tissue specific results", sort.condition="all", heatmap.profile=TRUE, heatmap.expression=FALSE, heatmap.unique.profile=FALSE, expressionMatrix=expressionSpeCondExample) ##Produce the Gene html page results for the first 20 genes using the specificResult object to be able to link ## these pages to the table result in the general html page specificResult=generalResult$specificResult genePageInfo=getGeneHtmlPage(expressionSpeCondExample, specificResult, name.index.html= "index_example_SpeCond_Results.html",outdir="Single_result_pages_example", gene.html.ids=c(1:20)) ##Produce the general html page results getFullHtmlSpeCondResult(L.specific.result=specificResult$L.specific.result, param.detection=specificResult$param.detection, page.name="Example_SpeCond_results2", page.title="Tissue specific results", prefix.file="S2", sort.condition="all", heatmap.profile=TRUE, heatmap.expression=FALSE, heatmap.unique.profile =FALSE, expressionMatrix=Mexp, gene.page.info=genePageInfo)