getData {RNAinteract} | R Documentation |
This function is the primary access function for a wide range of data from the screen. It does perform normalization, transformation, and reshaping if specified.
getData(sgi, type = "data", format = "plain", design = "template", mixTemplateQuery = TRUE, screen = NULL, channel = NULL, do.trafo = TRUE, do.inv.trafo = FALSE, normalized = FALSE, withoutgroups = c(), drop = TRUE)
sgi |
An object of class |
type |
Specifies which data is returned. Possible values are:
|
format |
The output format. Possible values:
|
design |
If type is one of the main effect types, the design can be specified to state if the "template" or "query" main effect is returned. |
mixTemplateQuery |
If TRUE, The template-query and query-template entries in the matrix are symmetrized. |
screen |
The screen names of which data should be returned. |
channel |
The channel names of which data should be returned. |
do.trafo |
Only effective, if type is "data". If TRUE, the data is transformed. |
do.inv.trafo |
Not effective if type is "data", "p.value", or "q.value". If TRUE, the values are back-transformed to the original scale. |
normalized |
If TRUE, the normalization data is returned. |
withoutgroups |
The genes from the specified groups are not returned in the data. |
drop |
If FALSE, the returned array is reduced in dimensions, whenever there is a dimension 1. |
An array containing the specified values is returned. In the case, the format is chosen to be "platelist", a list of matrices is returned.
Bernd Fischer
data("sgi") # get the original data, as plain file, reshaped in plate layout, # reshaped and summarized as target matrix D <- getData(sgi, type="data", do.inv.trafo = TRUE) Dplatelayout <- getData(sgi, type="data", format="platelist", do.inv.trafo = TRUE) splots::plotScreen(Dplatelayout[["1"]][["nrCells"]], nx=sgi@pdim[2], ny=sgi@pdim[1], ncol=3) Dmatrix <- getData(sgi, type="data", format="targetMatrix", do.inv.trafo = TRUE) # get main effects as plate layout with specified transformation # (usually log-transformed) Mplatelayout <- getData(sgi, type="main", design="template", screen="1", channel="nrCells", format="platelist") splots::plotScreen(Mplatelayout, nx=sgi@pdim[2], ny=sgi@pdim[1], ncol=3) # get non-interacting model and pairwise interaction scores as matrix NImatrix <- getData(sgi, type="ni.model", format="targetMatrix") PImatrix <- getData(sgi, type="pi", format="targetMatrix") PIplatelayout <- getData(sgi, type="main", design="query", screen="1", channel="nrCells", format="platelist") splots::plotScreen(PIplatelayout, nx=sgi@pdim[2], ny=sgi@pdim[1], ncol=3) # get p-values and q-values PVmatrix <- getData(sgi, type="p.value", format="targetMatrix") QVmatrix <- getData(sgi, type="q.value", format="targetMatrix")