# CMap Tools in R

## Documentation for package ‘cmapR’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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<- | 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<- | 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<- | 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