Function reference • creedenzymatic

All functions
`GCT-class`	An S4 class to represent a GCT object
`annotate.gct()`	Add annotations to a GCT object
`combine_tools()`	Combine data for quartile figure
`creedenzymatic()`	Runs Creedenzymatic
`.align_matrices()`	Align the rows and columns of two (or more) matrices
`.check_colnames()`	Check whether `test_names` are columns in the `data.frame` df
`.check_dups()`	Check for duplicates in a vector
`.extract.gct()`	Exract elements from a GCT matrix
`.is.wholenumber()`	Check if x is a whole number
`.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
`.read.gctx.ids()`	Read GCTX row or column ids
`.read.gctx.meta()`	Parse row or column metadata from GCTX files
`.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.gmt()`	Write a nested list to a GMT file
`.write.grp()`	Write a vector to a GRP file
`.write.tbl()`	Write a `data.frame` to a tab-delimited text file
`extract_top_kinases()`	Extract Top Kinases
`kinome_mp_file`	CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)
`kinome_mp_file_v1`	CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)
`kinome_mp_file_v2`	CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)
`kinome_mp_file_v3`	CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)
`kinome_mp_file_v4`	CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)
`melt.gct()`	Transform a GCT object in to a long form `data.table` (aka 'melt')
`merge.gct()`	Merge two GCT objects together
`ptk_pamchip_86402_array_layout_ptmsea`	CDRL Complete mapping of peptides - used for ptm-sea (PTK PamChip 86402)
`ptk_pamchip_86402_mapping`	CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)
`quartile_figure()`	Plot quartile Figure
`rank.gct()`	Convert a GCT object's matrix to ranks
`rank_kinases()`	Rank Kinases based on a score
`read_kea()`	Reads a dataframe of Peptides IDs and their Scores and run KEA3
`read_krsa()`	Reads and Rank KRSA table
`read_ptmsea()`	Reads a dataframe of Peptides IDs and their Scores and run PTM-SEA
`read_uka()`	Reads and Rank UKA table
`run_kea()`	Run KEA3 API based on a set of gene symbols
`run_ptmsea()`	Run PTM-SEA API using a gct file as input
`stk_pamchip_87102_array_layout_ptmsea`	CDRL Complete mapping of peptides - used for ptm-sea (STK PamChip 87102)
`stk_pamchip_87102_mapping`	CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)
`subset.gct()`	Subset a gct object using the provided row and column ids
`transpose.gct()`	Transpose a GCT object
`uka_db_full`	UKA Complete DB mapping File (STK + PTK)

Reference

All functions