Description Usage Arguments Details Value See Also Examples
View source: R/createOmics_Wrapper.R
This function calls the CreateOmicsPath
,
CreateOmicsSurv
, CreateOmicsReg
, and
CreateOmicsCateg
functions to create valid objects of the
classes OmicsPathway
, OmicsSurv
, OmicsReg
, or
OmicsCateg
, respectively.
1 2 3 4 5 6 7 8 9 |
assayData_df |
An N \times p data frame with named columns. |
pathwayCollection_ls |
A
If your gene pathways list is stored in a |
response |
An optional response object. See "Details" for more
information. Defaults to |
respType |
What type of response has been supplied. Options are
|
centerScale |
Should the values in |
minPathSize |
What is the smallest number of genes allowed in each pathway? Defaults to 3. |
... |
Dots for additional arguments passed to the internal
|
This function is a wrapper around the four CreateOmics*
functions. The values supplied to the response
function argument
can be in a list, data frame, matrix, vector, Surv
object, or any class which extends these. Because this function makes
"best guess" type conversions based on the respType
argument, this
argument is mandatory if response
is non-NULL
. Further, it
is the responsibility of the user to ensure that the coerced response
contained in the resulting Omics
object accurately reflects the
supplied response.
For respType = "survival"
, response
is assumed to be ordered
by event time, then event indicator. For example, if the response is a
data frame or matrix, this function assumes that the first column is the
time and the second column the death indicator. If the response is a list,
then this function assumes that the first entry in the list is the event
time and the second entry the death indicator. The death indicator must
be a logical or binary (0-1) vector, where 1 or TRUE
represents a
death and 0 or FALSE
represents right-censoring.
Some of the pathways in the supplied pathways list will be removed, or
"trimmed", during object creation. For the pathway-testing methods, these
trimmed pathways will have p-values given as NA
. For an
explanation of pathway trimming, see the documentation for the
IntersectOmicsPwyCollct
function.
A valid object of class OmicsPathway
, OmicsSurv
,
OmicsReg
, or OmicsCateg
.
OmicsPathway
,
CreateOmicsPath
,
OmicsSurv
,
CreateOmicsSurv
,
OmicsCateg
,
CreateOmicsCateg
OmicsReg
,
CreateOmicsReg
,
CheckAssay
,
CheckPwyColl
, and
IntersectOmicsPwyCollct
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 | ### Load the Example Data ###
data("colonSurv_df")
data("colon_pathwayCollection")
### Create an OmicsPathway Object ###
colon_OmicsPath <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection
)
### Create an OmicsSurv Object ###
colon_OmicsSurv <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection,
response = colonSurv_df[, 1:3],
respType = "surv"
)
### Create an OmicsReg Object ###
colon_OmicsReg <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection,
response = colonSurv_df[, 1:2],
respType = "reg"
)
### Create an OmicsCateg Object ###
colon_OmicsCateg <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection,
response = colonSurv_df[, c(1,3)],
respType = "cat"
)
|
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