Description Usage Arguments Value Methods (by generic) Slots Examples
Class ResultSet
used to encapsulate results from MEAL
and
omicrexposome
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | ## 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
.
1 | create_resultset("hello", list(), list(), list())
|
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