GCT                     Initialize an object of class 'GCT'
GCT-class               An S4 class to represent a GCT object
align_matrices          Align the rows and columns of two (or more)
                        matrices
annotate.gct            Add annotations to a GCT object
cdesc_char              An example table of metadata, as would be
                        parsed from or parse.gctx. Initially all the
                        columns are of type character.
check_colnames          Check whether 'test_names' are columns in the
                        'data.frame' df
check_dups              Check for duplicates in a vector
distil                  Collapse the rows or columns of a matrix using
                        weighted averaging
ds                      An example of a GCT object with row and column
                        metadata and gene expression values in the
                        matrix.
extract.gct             Exract elements from a GCT matrix
gene_set                An example collection of gene sets as used in
                        the Lamb 2006 CMap paper.
ids                     Extract the or set row or column ids of a GCT
                        object
is.wholenumber          Check if x is a whole number
kd_gct                  An example GCT object of knockdown experiments
                        targeting a subset of landmark genes.
lxb2mat                 Read an LXB file and return a matrix
mat                     Extract or set the matrix of GCT object
melt.gct                Transform a GCT object in to a long form
                        'data.table' (aka 'melt')
merge.gct               Merge two GCT objects together
meta                    Extract the or set metadata of a GCT object
na_pad_matrix           Pad a matrix with additional rows/columns of NA
                        values
parse.gctx              Parse a GCTX file into the workspace as a GCT
                        object
parse.gmt               Read a GMT file and return a list
parse.gmx               Read a GMX file and return a list
parse.grp               Read a GRP file and return a vector of its
                        contents
rank.gct                Convert a GCT object's matrix to ranks
read.gctx.ids           Read GCTX row or column ids
read.gctx.meta          Parse row or column metadata from GCTX files
robust_zscore           Compoute robust z-scores
subset.gct              Subset a gct object using the provided row and
                        column ids
threshold               Threshold a numeric vector
transpose.gct           Transpose a GCT object
update.gctx             Update the matrix of an existing GCTX file
write.gct               Write a GCT object to disk in GCT format
write.gctx              Write a GCT object to disk in GCTX format
write.tbl               Write a 'data.frame' to a tab-delimited text
                        file
write_gmt               Write a nested list to a GMT file
write_grp               Write a vector to a GRP file
