IntersectOmicsPwyCollct | R Documentation |
Given a bio-assay design matrix and a pathwayCollection
gene pathways list (each within an Omics*
-class object), delete
the genes / proteins / lipids / metabolomes / transcriptomes symbols or
IDs recorded in each pathway which are not recorded in the assay data
frame.
IntersectOmicsPwyCollct(object, trim = 3, message = TRUE, ...)
## S4 method for signature 'OmicsPathway'
IntersectOmicsPwyCollct(object, trim = 3, message = TRUE, ...)
object |
An object of class |
trim |
The minimum cutoff of matching -Ome measures before a pathway is excluded. Defaults to 3. |
message |
Should this function return diagnostic messages? Messages
concern the percentage of genes included in the pathways list but not
measured in the data, genes measured in the data but not called for in the
pathways, and the number of pathways ignored due to too few number of
genes present after trimming. Defaults to |
... |
Dots for additional internal arguments (as necessary). |
This function takes in a data frame with named columns and a
pathwayCollection
list, all through one of the Omics*
classes. This function will then copy the pathway collection, iterate over
the list of copied pathways, delete symbols or IDs from that pathway
without matches from the bio-assay design matrix column names, and remove
any pathways that have fewer than trim
genes with corresponding
columns in the assay. The genes not recorded in the bio-assay design
matrix are removed from the copy of the pathway collection (the
trimPathwayCollection
object), but remain in the original pathway
collection.
NOTE: some genes will be included in more than one pathway, so these
pathways are not mutually exclusive. Further note that there may be many
genes in the assay design matrix that are not included in the pathway
sets, so these will not be extracted to the list. It is then vitally
important to use either a very broad and generic pathwayCollection
list or a pathwayCollection
list that is appropriate for the assay
data supplied. While you can create your own pathway lists, create proper
pathwayCollection
list objects by importing .gmt
files with
the read_gmt
function.
A valid Omics*
-class object. This output object will be
identical to the input object, except that any genes present in the
pathways list, but not present in the MS design matrix, will have been
removed. Additionally, the pathway list will have the number of genes in
each trimmed pathway stored as the n_tested
object.
# DO NOT CALL THIS FUNCTION DIRECTLY. USE CreateOmics() INSTEAD.
## Not run:
### Load the Example Data ###
data("colonSurv_df")
data("colon_pathwayCollection")
### Create an OmicsSurv Object ###
colon_Omics <- CreateOmics(
assayData_df = colonSurv_df[, -(2:3)],
pathwayCollection_ls = colon_pathwayCollection
)
## End(Not run)
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