Package: cmapR 1.25.0

Ted Natoli

cmapR: CMap Tools in R

The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.

Authors:Ted Natoli [aut, cre]

cmapR_1.25.0.tar.gz
cmapR_1.25.0.zip(r-4.7)cmapR_1.25.0.zip(r-4.6)cmapR_1.25.0.zip(r-4.5)
cmapR_1.25.0.tgz(r-4.6-any)cmapR_1.25.0.tgz(r-4.5-any)
cmapR_1.25.0.tar.gz(r-4.7-any)cmapR_1.25.0.tar.gz(r-4.6-any)
cmapR_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cmapR/json (API)

# Install 'cmapR' in R:

install.packages('cmapR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cmap/cmapr/issues

Datasets:

cdesc_char - An example table of metadata, as would be parsed from or parse.gctx. Initially all the columns are of type character.
ds - An example of a GCT object with row and column metadata and gene expression values in the matrix.
gene_set - An example collection of gene sets as used in the Lamb 2006 CMap paper.
kd_gct - An example GCT object of knockdown experiments targeting a subset of landmark genes.

On BioConductor:cmapR-1.25.0(bioc 3.24)cmapR-1.24.0(bioc 3.23)

dataimport datarepresentation geneexpression bioconductor bioinformatics cmap

9.01 score 94 stars 404 scripts 3 mentions 52 exports 30 dependencies

Last updated from:031c9df8d5. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	182
linux-devel-x86_64	NOTE	345
source / vignettes	OK	214
linux-release-x86_64	NOTE	370
macos-release-arm64	NOTE	179
macos-oldrel-arm64	NOTE	150
windows-devel	NOTE	231
windows-release	NOTE	224
windows-oldrel	NOTE	214
wasm-release	OK	166

Exports:align_matrices annotate_gct annotate.gct append.dim check_colnames check_dups distil extract_gct extract.gct fix.datatypes GCT ids ids<-is.wholenumber lxb2mat mat mat<-melt_gct melt.gct merge_gct meta meta<-na_pad_matrix parse_gctx parse_gmt parse_gmx parse_grp parse.gctx parse.gmt parse.gmx parse.grp rank_gct rank.gct read_gctx_ids read_gctx_meta read.gctx.ids read.gctx.meta robust_zscore subset_gct threshold transpose_gct transpose.gct update_gctx write_gct write_gctx write_gmt write_grp write_tbl write.gct write.gctx write.gctx.meta write.tbl

Dependencies:abind BH Biobase BiocGenerics biocmake cpp11 cytolib data.table DelayedArray dir.expiry filelock flowCore generics GenomicRanges IRanges lattice Matrix MatrixGenerics matrixStats Rcpp rhdf5 rhdf5filters Rhdf5lib RProtoBufLib S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector

cmapR Tutorial

Rendered fromtutorial.Rmdusingknitr::rmarkdown

Last update: 2023-04-03
Started: 2020-01-14

Citation

Development and contributors

Readme and manuals

Help Manual

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