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b/man/bipartite_peaks2genes.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/bipartites.R |
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\name{bipartite_peaks2genes} |
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\alias{bipartite_peaks2genes} |
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\title{Compute links between DNA regions and genenames} |
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\usage{ |
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bipartite_peaks2genes( |
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hummus_object, |
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gene_assay = "RNA", |
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peak_assay = "peaks", |
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gene_multiplex_name = NULL, |
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peak_multiplex_name = NULL, |
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peak_to_gene_method = "Signac", |
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upstream = 500, |
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downstream = 500, |
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only_tss = TRUE, |
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store_network = FALSE, |
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output_file = NULL, |
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bipartite_name = "atac_rna" |
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) |
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} |
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\arguments{ |
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\item{hummus_object}{(hummus_object) - Hummus object.} |
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\item{gene_assay}{(character) - Name of assay containing the gene expression |
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data. Default: "RNA".} |
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\item{peak_assay}{(character) - Name of the assay containing the DNA regions |
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(ATAC peaks). Default: "peaks".} |
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\item{gene_multiplex_name}{(character) - Name of the multiplex containing the |
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genes. |
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If NULL, the name of the gene assay is used.} |
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\item{peak_multiplex_name}{(character) - Name of the multiplex containing the |
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DNA regions (ATAC peaks). If NULL, the name of the peak assay is used.} |
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\item{peak_to_gene_method}{(character) - Method to use to compute the links |
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between peaks and genes. Default: "Signac". |
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\itemize{ |
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\item \code{'Signac'} - Use Signac::Extend to extend genes. |
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\item \code{'GREAT'} - Not implemented yet. |
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}} |
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\item{upstream}{(int) - Upstream distance from TSS |
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to consider as potential promoter.} |
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\item{downstream}{(int) - Downstream distance from TSS |
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to consider as potential promoter.} |
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\item{only_tss}{(logical) - If TRUE, only TSS will be considered.} |
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\item{store_network}{(bool) - Save the bipartite directly |
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(\code{TRUE}, default) or return without saving on disk (\code{FALSE}).} |
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\item{output_file}{(character) - Name of the output_file |
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(if store_bipartite == \code{TRUE}). Default: NULL.} |
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\item{bipartite_name}{(character) - Name of bipartite. Default: "atac_rna".} |
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\item{verbose}{(integer) Display function messages. |
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Set to 0 for no message displayed, >= 1 for more details. Default: 1.} |
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} |
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\value{ |
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hummus_object (hummus_object) - Hummus object w/ atac-rna bipartite |
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added to the multilayer slot |
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} |
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\description{ |
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Compute and add bipartite between DNA regions and genenames to hummus object. |
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Links are computed based on the distance between peaks and gene's TSS |
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location from gene.range annotations. |
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Call find_peaks_near_genes function, that can use different methods. |
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} |
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\examples{ |
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hummus <- bipartite_peaks2genes( |
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hummus_object = hummus, |
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gene_assay = "RNA", |
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peak_assay = "peaks", |
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gene_multiplex_name = "RNA", |
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peak_multiplex_name = "peaks", |
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peak_to_gene_method = "Signac", |
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upstream = 500, |
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downstream = 500, |
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only_tss = TRUE, |
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store_network = FALSE, |
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bipartite_name = "atac_rna") |
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} |