ResultSet {MultiDataSet} | R Documentation |
Class ResultSet
used to encapsulate results from MEAL
and
omicrexposome
.
## S4 method for signature 'ResultSet' fData(object) ## S4 method for signature 'ResultSet' getAssociation(object, rid = 1, coef = 2, contrast = NULL, fNames = NULL, ...) ## S4 method for signature 'ResultSet' length(x) ## S4 method for signature 'ResultSet' names(x) ## S4 method for signature 'ResultSet' opt(object) ## S4 method for signature 'ResultSet,ANY' plot( x, y, rid = 1, coef = 2, contrast = NULL, type, tFC = 2, tPV = -log10(0.001), show.labels = TRUE, show.effect = FALSE, show.lambda = TRUE, fNames = c("chromosome", "start"), subset, highlight, ... ) ## S4 method for signature 'ResultSet' varLabels(object) create_resultset(fOrigin, lResults, fData, lOptions = list())
object |
A |
rid |
Name or index of the internal result to be used |
coef |
Coefficient to be returne, usually 2 |
contrast |
Numeric matrix with the contrasts used to perform the analyses |
fNames |
Character vector with the names of the fData columns that will be added to the results data.frame. |
... |
Further arguments passed to topTable |
x |
A |
y |
- |
type |
Type of plot to be drawn |
tFC |
Threshold for log FC of effect |
tPV |
Threshold for P-Value |
show.labels |
(default |
show.effect |
(default: |
show.lambda |
(default: |
subset |
GenomicRanges used to zoom a region in Manhattan plot |
highlight |
GenomicRanges used to highlight a region in Manhattan plot |
fOrigin |
Chracter with the function used to run the analysis. |
lResults |
List with the results |
fData |
List with the feature data. |
lOptions |
List with additional options |
An object of class ResultSet
fData
: Returns data.frame
with feature's data.
getAssociation
: Getter to obtain the raw data.frame
from
association and integration analysis.
length
: Returns the amoung of analyses stored in the
ResultSet
.
names
: Returns the names of the omics data used to create
the ResultSet
.
opt
: Returns a list with the options used to create the
ResultSet
plot
: Allows to plot a series of plots (QQ plot, Manhattan
plot and Volcano plot) depending on the results stored in the
ResultSet
.
varLabels
: Returns the names of the variables of the models used in
a ResultSet
.
fun_origin
Character containing the function that creates the object.
results
List containing the results of the association/integration.
fData
List containing the feature-data of the original objects.
options
list of options used to create the ResultSet
.
create_resultset("hello", list(), list(), list())