Exract elements from a GCT matrix

extract the elements from a GCT object where the values of row_field and col_field are the same. A concrete example is if g represents a matrix of signatures of genetic perturbations, and you wan to extract all the values of the targeted genes.

.extract.gct(
  g,
  row_field,
  col_field,
  rdesc = NULL,
  cdesc = NULL,
  row_keyfield = "id",
  col_keyfield = "id"
)

Arguments

g	the GCT object
row_field	the column name in rdesc to search on
col_field	the column name in cdesc to search on
rdesc	a data.frame of row annotations
cdesc	a data.frame of column annotations
row_keyfield	the column name of rdesc to use for annotating the rows of g
col_keyfield	the column name of cdesc to use for annotating the rows of g

Value

a list of the following elements

mask

a logical matrix of the same dimensions as ds@mat indicating which matrix elements have been extracted

idx

an array index into ds@mat representing which elements have been extracted

vals

a vector of the extracted values