Man pages for cmap/cmapR
CMap Tools in R

align_matricesAlign the rows and columns of two (or more) matrices
annotate_gctAdd annotations to a GCT object
append_dimAppend matrix dimensions to filename
cdesc_charAn example table of metadata, as would be parsed from or...
check_colnamesCheck whether 'test_names' are columns in the 'data.frame' df
check_dupsCheck for duplicates in a vector
distilCollapse the rows or columns of a matrix using weighted...
dsAn example of a GCT object with row and column metadata and...
extract_gctExract elements from a GCT matrix
fix_datatypesAdjust the data types for columns of a meta data frame
GCT-classAn S4 class to represent a GCT object
gene_setAn example collection of gene sets as used in the Lamb 2006...
get_gct_idsExtract the ids from a GCT object
get_gct_matrixExtract the matrix from a GCT object
get_gct_metaExtract the metadata from a GCT object
is.wholenumberCheck if x is a whole number
kd_gctAn example GCT object of knockdown experiments targeting a...
lxb2matRead an LXB file and return a matrix
melt_gctTransform a GCT object in to a long form 'data.table' (aka...
merge_gctMerge two GCT objects together
merge_with_precedenceMerge two 'data.frame's, but where there are common fields...
na_pad_matrixPad a matrix with additional rows/columns of NA values
parse_gctxParse a GCTX file into the workspace as a GCT object
parse_gmtRead a GMT file and return a list
parse_gmxRead a GMX file and return a list
parse_grpRead a GRP file and return a vector of its contents
process_idsReturn a subset of requested GCTX row/colum ids out of the...
rank_gctConvert a GCT object's matrix to ranks
read_gctx_idsRead GCTX row or column ids
read_gctx_metaParse row or column metadata from GCTX files
robust_zscoreCompoute robust z-scores
subset_gctSubset a gct object using the provided row and column ids
subset_to_idsDo a robust 'data.frame' subset to a set of ids
thresholdThreshold a numeric vector
transpose_gctTranspose a GCT object
update_gctxUpdate the matrix of an existing GCTX file
write_gctWrite a GCT object to disk in GCT format
write_gctxWrite a GCT object to disk in GCTX format
write_gctx_metaWrite a 'data.frame' of meta data to GCTX file
write_gmtWrite a nested list to a GMT file
write_grpWrite a vector to a GRP file
write_tblWrite a 'data.frame' to a tab-delimited text file
cmap/cmapR documentation built on Jan. 26, 2020, midnight