Man pages for SingerLab/gac
Genetic Analysis of Cells

addCellsAdd cells to an existing cnr
addGeneInfoAdds Gene Information to the gene.index
addInfoAdds info to the chromInfo
add_in_silico_rootbuild an in-silico root cell and clone profile
addPhenoAdds additional phenotypes for a new trait
avg_num_alleles_per_locusEstimate the estimated number of alleles (copies) per locus
binary.cnrbuild binary CNR from integer copy number data
binary.Xbuild binary matrix from integer copy number data
buildCNRBuild a CNR bundle (Copy Number, -Rounded)
callCNCopy number call categories from ratio data
callDNA_CNcall copy numbers out of CNR data
chr_breaksestimate chromosome end locations along a continuous genome
chr_colorschromosome colors
chromInfoChromosome coordinates and additional data of the bins
cluster_heterogeneitycluster heterogeneity across the sample
cnrcnr: copy number, rounded
copynumbersCopy number quantal matrix (copynumbers)
create_chromosome_annotationcreate chromosome annotations for custom heatmaps
create_chromosome_annotation_bottomcreate chromosome annotations for custom heatmaps
create_chromosome_annotation_leftcreate chromosome annotations for custom heatmaps
create_chromosome_annotation_rightcreate chromosome annotations for custom heatmaps
create_chromosome_annotation_topcreate chromosome annotations for custom heatmaps
dnadna: a cnr with bulk DNA like copy number data
doKSpectralRun Specral K to select optimum and maximum K from Consensus...
estimate_joint_effectsWrapper to joint CNA effect estimation using GLMNet
excludeCellsexclude cells from CNR bundle
expand2genesExpands the bins to genes
export_cnrexport CNR to flat text files
export_pval_igvExport the p-values for comparisons of interest to visualize...
genotype_vdjGenotype cells at the VDJ recombination sites
get_alteration_frequenciesestimate bin and gene alteration frequencies
get_cluster_profilesBuild a consensus copy number profile for each cluster or...
grch37.genes.5kBin-to-gene index
hg19_cytoBandHG19 cytoband file from UCSC genome browser
histo_logitPerform logistic regression for a binary/binarized trait
histo_logit_covperform logistic regression for a binary/binarized trait with...
keepCellskeep cells from CNR bundle
list_genes_in_regionfinds genes within one chromosome interval
list_gene_symbolslist out genes
lookupCNLookup copy number data from bins
mapdMedian absolute pairwise deviance (MAPD)
mark.genesMark genes
maximum.percentageMax percent
mid_chrestiamte chromosome midpoint locations along a continuous...
minimum.intersectMinimum tree.height at the intersect of one-cell and...
nbinsnumber of bins
ncellsnumber of cells in cnr
ngenesnumber of genes in gene.index
nphenonumber of phenotypes
optClustoptimizing clustering for single-cell copy number
order_binsorder genome bins based on chromosome and starting position
order_genesorder gene.index based on chromosome and starting coordinate
parctanPeter Andrew's arctan transformation for visualizing copy...
phenoSingle-cell phenotype annotation
phylo_cnrCalculating cell-to-cell distances, heirarchical clustering,...
phylo_ddrcCalculating clone-to-clone distances, and estimating a...
plot_ccpplot consensus clustering
plotCLplot cluster optimization
plot_cn_correlationsplot genome wide correlations
plot_effectGenome-wide effects plot
plot_frequenciesplot genome-wide amplification and deletion frequencies
plot_lrManhattan plot of logistic regression output
plot_sKplot kCC vs sK plot kParameter, and stable K from kStats
proportion_of_polymorphic_lociproportion of polymorphic alleles as subclonal
pull_gene_copy_numberspull a set of copy numbers from a cnr into a data.frame
pull_gene_detailsPull gene details for a set of genes
qcQuality control annotation
rank_clonesrank clones
rle_ddrcrun length encoding to create segment files from DDRC.df
roundCNRrounded quantal matrix
run_consensus_clusteringrun consensus clustering
seg2binsconvert .seg files to match a chromInfo matrix
setBrayClustersSet Bray clusters
setKccSet cluster membership for K clusters
split_cnrsplit a cnr by one variable
subsetCNRSubset a set of bins or genes from a CNR object
summary_cnrsummary of cnr bundle
sync_cnrsync cnr cells to those in the phenotype annotation
vdjBrayClustVDJ cells clustering based on Bray-Curtis Dissimilarity
vdjHeatmapHeatmap of cells with VDJ recombination
vdjPlotClustplot VDJ clustering
SingerLab/gac documentation built on Feb. 12, 2024, 9:32 a.m.