CMap Tools in R

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Documentation for package ‘cmapR’ version 1.0.0

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align_matrices Align the rows and columns of two (or more) matrices
annotate.gct Add annotations to a GCT object
annotate_gct Add annotations to a GCT object
annotate_gct-method 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
extract_gct Exract elements from a GCT matrix
GCT Initialize an object of class 'GCT'
GCT-class An S4 class to represent a GCT object
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
ids-method Extract the or set row or column ids of a GCT object
ids<--method 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
mat-method Extract or set the matrix of GCT object
mat<--method Extract or set the matrix of GCT object
melt.gct Transform a GCT object in to a long form 'data.table' (aka 'melt')
melt_gct Transform a GCT object in to a long form 'data.table' (aka 'melt')
melt_gct-method Transform a GCT object in to a long form 'data.table' (aka 'melt')
merge.gct Merge two GCT objects together
merge_gct Merge two GCT objects together
merge_gct-method Merge two GCT objects together
meta Extract the or set metadata of a GCT object
meta-method Extract the or set metadata of a GCT object
meta<--method 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
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
rank_gct Convert a GCT object's matrix to ranks
rank_gct-method 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
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
subset_gct Subset a gct object using the provided row and column ids
subset_gct-method Subset a gct object using the provided row and column ids
threshold Threshold a numeric vector
transpose.gct Transpose a GCT object
transpose_gct Transpose a GCT object
transpose_gct-method Transpose a GCT object
update.gctx Update the matrix of an existing GCTX file
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_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