annotate.gct {cmapR} | R Documentation |
Given a GCT object and either a data.frame
or
a path to an annotation table, apply the annotations to the
gct using the given keyfield
.
annotate.gct(...) annotate_gct(g, annot, dim = "row", keyfield = "id") ## S4 method for signature 'GCT' annotate_gct(g, annot, dim = "row", keyfield = "id")
... |
arguments passed on to |
g |
a GCT object |
annot |
a |
dim |
either 'row' or 'column' indicating which dimension
of |
keyfield |
the character name of the column in |
a GCT object with annotations applied to the specified dimension
Other GCT utilities:
melt.gct()
,
merge.gct()
,
rank.gct()
,
subset.gct()
gct_path <- system.file("extdata", "modzs_n25x50.gctx", package="cmapR") # read the GCT file, getting the matrix only g <- parse_gctx(gct_path, matrix_only=TRUE) # separately, read the column annotations and then apply them using # annotate_gct cdesc <- read_gctx_meta(gct_path, dim="col") g <- annotate_gct(g, cdesc, dim="col", keyfield="id")