get_region_for_gene: getRegionForGene

In manschmi/RMetaTools: Tools For Metagene Analysis

Description

gets region for a specified gene.

Usage

get_region_for_gene(
  anno,
  gene_id = "",
  gene_name = "",
  anchor = "gene",
  left_offset = 0,
  right_offset = 0
)

Arguments

anno	a data.frame holding the annotations
gene_name	alternative if id is not provided. Default =”.
anchor	region around gene, TSS or TES. Default ='gene'.
left_offset	extend by this upstream start or anchor
right_offset	extend by this downstream end or anchor
id	id of the gene. Default =”.

Details

Retrieves the information in a named vector.

Value

A named vector.

Examples

anno_gencode <- read.table('/Users/schmidm/Documents/other_people_to_and_from/ClaudiaI/bw/gencode_v23_hg19_genes.bed', col.names = c('chr', 'start', 'end', 'id', 'type', 'strand', 'name'))
region <- get_region_for_gene(anno_gencode, gene_name='GAPDH', anchor='TSS', 2000, 5000)
files <- create_bw_file_set(path, c('[y,I]','rep[3,4]', '.bw$'), c('_N20', '_3D12'), c('siRNA', 'ab', 'rep'), '_')
set <- load_bw_set(files, region)
ggplot(set, aes(x=starts, y=scores, color=rep)) + geom_line() + facet_grid(siRNA~ab)

region <- get_region_for_gene(anno_gencode, gene_name='HIST1H4C', anchor='gene', left_offset=2000, right_offset=5000)
files <- create_bw_file_set(path, c('[y,I]','rep[3,4]', '.bw$'), c('_N20', '_3D12'), c('siRNA', 'ab', 'rep'), '_')
set <- load_bw_set(files, region)
ggplot(set, aes(x=starts, y=scores, color=rep)) + geom_line() + facet_grid(siRNA~ab)
ggplot(set, aes(x=starts, y=scores, color=siRNA)) + geom_line() + facet_grid(.~ab)

scaled_set <- set %>% group_by(siRNA, ab, rep) %>% mutate(scores=scale(scores))
ggplot(scaled_set, aes(x=starts, y=scores, color=siRNA)) + geom_line() + facet_grid(.~ab)

manschmi/RMetaTools documentation built on Dec. 14, 2021, 4:33 a.m.