pathwayCollection Values in Omics*
Objectsget_set_OmicsPathway.Rd"Get" or "Set" the values of the assayData_df,
sampleIDs_char, or pathwayCollection slots of an object of
class OmicsPathway or a class that extends this class
(OmicsSurv, OmicsReg, or OmicsCateg).
getAssay(object, ...) getAssay(object) <- value getSampleIDs(object, ...) getSampleIDs(object) <- value getPathwayCollection(object, ...) getPathwayCollection(object) <- value getTrimPathwayCollection(object, ...) # S4 method for OmicsPathway getAssay(object, ...) # S4 method for OmicsPathway getAssay(object) <- value # S4 method for OmicsPathway getSampleIDs(object, ...) # S4 method for OmicsPathway getSampleIDs(object) <- value # S4 method for OmicsPathway getPathwayCollection(object, ...) # S4 method for OmicsPathway getPathwayCollection(object) <- value # S4 method for OmicsPathway getTrimPathwayCollection(object, ...)
| object | An object of or extending |
|---|---|
| ... | Dots for additional internal arguments (currently unused). |
| value | The replacement object to be assigned to the specified slot. |
The "get" functions return the objects in the slots specified:
getAssay returns the assayData_df data frame object,
getSampleIDs returns the sampleIDs_char character vector,
getPathwayCollection returns the pathwayCollection list
object, and getTrimPathwayCollection returns the
trimPathwayCollection. These functions can extract these values
from any valid OmicsPathway, OmicsSurv, OmicsReg, or
OmicsCateg object.
The "set" functions enable the user to edit or replace objects in the
assayData_df, sampleIDs_char, or pathwayCollection
slots for any OmicsPathway, OmicsSurv, OmicsReg, or
OmicsCateg objects, provided that the new values do not violate
the validity checks of their respective objects. Because the slot for
trimPathwayCollection is filled upon object creation, and to ensure
that this pathway collection is "clean", there is no "set" function for
the trimmed pathway collection slot. Instead, users can update the pathway
collection, and the trimmed pathway collection will be updated
automatically. See "Details" for more information on the "set" functions.
These functions can be useful to set or extract the assay data or
pathways list from an Omics*-class object. However, we recommend
that users simply create a new, valid Omics* object instead of
modifying an existing one. The validity of edited objects is checked with
the ValidOmicsSurv, ValidOmicsCateg, or
ValidOmicsReg functions.
Further, because the pathwayPCA methods require a cleaned (trimmed)
pathway collection, the trimPathwayCollection slot is read-only.
Users may only edit this slot by updating the pathway collection provided
to the pathwayCollection slot. Despite this functionality, we
strongly recommend that users create a new object with the
updated pathway collection, rather than attempting to overwrite the slots
within an existing object. See IntersectOmicsPwyCollct for
details on trimmed pathway collection.
data("colonSurv_df") data("colon_pathwayCollection") colon_Omics <- CreateOmics( assayData_df = colonSurv_df[, -(2:3)], pathwayCollection_ls = colon_pathwayCollection )#> #>#>#>#> #> #>#> #> #>getAssay(colon_Omics)#> # A tibble: 250 x 656 #> JUN SOS2 PAK3 RAF1 PRKCB BTC SHC1 PRKCA ELK1 NRG1 #> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 -0.880 0.367 1.30 0.480 -0.867 -0.790 -2.84e-1 0.0104 1.04 0.670 #> 2 -1.11 2.15 1.62 0.165 0.547 -0.261 -4.91e-4 1.18 1.49 1.30 #> 3 -0.752 0.764 0.330 -0.541 0.164 0.452 6.91e-1 -0.950 0.667 0.128 #> 4 1.03 -0.751 2.75 -0.878 -1.09 -0.481 -1.34e+0 1.52 2.23 3.65 #> 5 -1.73 0.613 2.66 0.550 0.197 -1.02 1.56e-1 -1.29 1.68 -2.15 #> 6 -0.162 0.126 -0.324 0.627 -0.106 -1.17 1.11e+0 -1.27 0.964 1.79 #> 7 -0.980 -0.520 1.28 -0.343 -0.762 -0.489 -2.57e-1 0.0518 1.21 -0.312 #> 8 0.616 0.0633 0.343 -0.0195 0.578 -1.37 6.38e-1 1.37 1.05 -0.703 #> 9 1.35 -0.467 -0.149 -0.718 -0.898 0.527 -6.04e-2 1.32 -1.00 -0.266 #> 10 -0.538 0.413 -0.503 -1.27 -0.466 0.178 3.45e-1 -1.40 -0.378 0.0623 #> # … with 240 more rows, and 646 more variables: PAK2 <dbl>, MTOR <dbl>, #> # PAK4 <dbl>, MAP2K4 <dbl>, EIF4EBP1 <dbl>, BAD <dbl>, PRKCG <dbl>, #> # NRG3 <dbl>, MAPK9 <dbl>, ERBB4 <dbl>, MAPK10 <dbl>, PTK2 <dbl>, #> # ERBB2 <dbl>, ERBB3 <dbl>, MAP2K2 <dbl>, TGFA <dbl>, BRAF <dbl>, #> # MAP2K1 <dbl>, MAP2K7 <dbl>, ABL1 <dbl>, NRG2 <dbl>, AKT1 <dbl>, ABL2 <dbl>, #> # AKT2 <dbl>, SHC4 <dbl>, RPS6KB1 <dbl>, RPS6KB2 <dbl>, AKT3 <dbl>, #> # NRAS <dbl>, GRB2 <dbl>, AREG <dbl>, STAT5B <dbl>, MAPK3 <dbl>, #> # STAT5A <dbl>, PAK6 <dbl>, SOS1 <dbl>, MYC <dbl>, MAPK1 <dbl>, NCK1 <dbl>, #> # PIK3R5 <dbl>, NRG4 <dbl>, HRAS <dbl>, MAPK8 <dbl>, EGFR <dbl>, GSK3B <dbl>, #> # CBLB <dbl>, KRAS <dbl>, CBL <dbl>, SHC3 <dbl>, CDKN1B <dbl>, CDKN1A <dbl>, #> # EGF <dbl>, EREG <dbl>, ARAF <dbl>, NCK2 <dbl>, SRC <dbl>, PIK3R3 <dbl>, #> # CAMK2A <dbl>, CAMK2B <dbl>, CAMK2D <dbl>, CAMK2G <dbl>, PAK1 <dbl>, #> # CBLC <dbl>, CRK <dbl>, PIK3CA <dbl>, PIK3CB <dbl>, CRKL <dbl>, #> # PIK3CD <dbl>, GAB1 <dbl>, PLCG1 <dbl>, PLCG2 <dbl>, SHC2 <dbl>, #> # HBEGF <dbl>, PIK3CG <dbl>, PIK3R1 <dbl>, PIK3R2 <dbl>, EPHB2 <dbl>, #> # EPHB4 <dbl>, EFNA5 <dbl>, PXN <dbl>, CDC42 <dbl>, EFNB3 <dbl>, RRAS <dbl>, #> # GRB7 <dbl>, SYNJ1 <dbl>, EPHB3 <dbl>, EFNB1 <dbl>, DNM1 <dbl>, #> # MAP4K4 <dbl>, GRIA1 <dbl>, EPHB1 <dbl>, ROCK1 <dbl>, ITSN1 <dbl>, #> # RAP1A <dbl>, RAC1 <dbl>, RAP1B <dbl>, EFNB2 <dbl>, WASL <dbl>, TF <dbl>, #> # KALRN <dbl>, …getPathwayCollection(colon_Omics)#> Object with Class(es) 'pathwayCollection', 'list' [package 'pathwayPCA'] with 3 elements: #> $ pathways:List of 15 #> $ TERMS : Named chr [1:15] "KEGG_PENTOSE_PHOSPHATE_PATHWAY" ... #> $ setsize : Named int [1:15] 27 64 ...