Usage
DEXSeqHTML(object, genes=NULL, path="DEXSeqReport", file="testForDEU.html", fitExpToVar="condition", FDR=0.1, color=NULL, color.samples=NULL, mart="", filter="", attributes="", extraCols=NULL, BPPARAM=MulticoreParam(workers=1))
Arguments
object
An DEXSeqResults object
genes
A character vector of gene identifiers
to be included in the report. If NULL,
the genes included in the report will
be the significant hits at the given
false discovery rate. See "FDR" below.
path
A path in the system where to write the
report.
file
The name of the html file.
fitExpToVar
A variable contained in the design of the ecs; the counts
will be fitted to this variable to get the plotting values.
FDR
A false discovery rate
color
A vector of colors, one for each of the levels of the
values of "fitExpToVar".
color.samples
A vector of colors for each of the samples. If NULL, the colors
of each sample will be asigned according to its corresponding
condition. Useful to visualize complex experimental designs.
mart
object of class Mart, created with the useMart function,
with dataset specified
filter
Filters (ONLY ONE) that should be used in the query. A
possible list of filters can be retrieved using the function
listFilters. Please note that the value of this filter will
always be the geneIDs in the DEXSeqResults object.
attributes
Attributes you want to retrieve. A possible list of
attributes can be retrieved using the biomaRt function
listAttributes.
extraCols
A data frame with one or more columns to add to the report.
For example, additional information about the genes. The data frame
should be indexed by the gene names of the ExonCountSet object,
e.g. the rownames of the data frame should correspond to the gene
names.
BPPARAM
A 'BiocParallelParam' instance.
See ?bplapply
for details.