Package: cmapR 1.17.0

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_1.17.0.tar.gz
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cmapR.pdf |cmapR.html✨
cmapR/json (API)
NEWS

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

Peer review:

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-1.17.0(bioc 3.20)cmapR-1.16.0(bioc 3.19)

bioconductor-package

52 exports 1.80 score 38 dependencies 3 mentions

Last updated 2 months agofrom:f48edb8368

Exports:align_matricesannotate_gctannotate.gctappend.dimcheck_colnamescheck_dupsdistilextract_gctextract.gctfix.datatypesGCTidsids<-is.wholenumberlxb2matmatmat<-melt_gctmelt.gctmerge_gctmetameta<-na_pad_matrixparse_gctxparse_gmtparse_gmxparse_grpparse.gctxparse.gmtparse.gmxparse.grprank_gctrank.gctread_gctx_idsread_gctx_metaread.gctx.idsread.gctx.metarobust_zscoresubset_gctthresholdtranspose_gcttranspose.gctupdate_gctxwrite_gctwrite_gctxwrite_gmtwrite_grpwrite_tblwrite.gctwrite.gctxwrite.gctx.metawrite.tbl

Dependencies:abindaskpassBHBiobaseBiocGenericscpp11crayoncurlcytolibdata.tableDelayedArrayflowCoreGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6Rcpprhdf5rhdf5filtersRhdf5libRProtoBufLibS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

cmapR Tutorial

Ted Natoli

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Jul 02 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Align the rows and columns of two (or more) matricesalign_matrices
Add annotations to a GCT objectannotate.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' dfcheck_colnames
Check for duplicates in a vectorcheck_dups
Collapse the rows or columns of a matrix using weighted averagingdistil
An example of a GCT object with row and column metadata and gene expression values in the matrix.ds
Exract elements from a GCT matrixextract.gct extract_gct
Initialize an object of class 'GCT'GCT
An S4 class to represent a GCT objectGCT-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 objectids ids,GCT-method ids<- ids<-,GCT-method
Check if x is a whole numberis.wholenumber
An example GCT object of knockdown experiments targeting a subset of landmark genes.kd_gct
Read an LXB file and return a matrixlxb2mat
Extract or set the matrix of GCT objectmat 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 togethermerge.gct merge_gct merge_gct,GCT,GCT-method
Extract the or set metadata of a GCT objectmeta meta,GCT-method meta<- meta<-,GCT-method
Pad a matrix with additional rows/columns of NA valuesna_pad_matrix
Parse a GCTX file into the workspace as a GCT objectparse.gctx parse_gctx
Read a GMT file and return a listparse.gmt parse_gmt
Read a GMX file and return a listparse.gmx parse_gmx
Read a GRP file and return a vector of its contentsparse.grp parse_grp
Convert a GCT object's matrix to ranksrank.gct rank_gct rank_gct,GCT-method
Read GCTX row or column idsread.gctx.ids read_gctx_ids
Parse row or column metadata from GCTX filesread.gctx.meta read_gctx_meta
Compoute robust z-scoresrobust_zscore
Subset a gct object using the provided row and column idssubset.gct subset_gct subset_gct,GCT-method
Threshold a numeric vectorthreshold
Transpose a GCT objecttranspose.gct transpose_gct transpose_gct,GCT-method
Update the matrix of an existing GCTX fileupdate.gctx update_gctx
Write a nested list to a GMT filewrite_gmt
Write a vector to a GRP filewrite_grp
Write a GCT object to disk in GCT formatwrite.gct write_gct
Write a GCT object to disk in GCTX formatwrite.gctx write_gctx
Write a 'data.frame' to a tab-delimited text filewrite.tbl write_tbl