metagene_rel_anchor: Compute Metagene Values For Region Around A Reference-point

In manschmi/RMetaTools: Tools For Metagene Analysis

Description

Computes a metagene object from scratch, similar to metagene_matrix but as more compact form.

Usage

metagene_rel_anchor(
  bw_plus,
  bw_minus,
  anno,
  anchor = "TSS",
  upstream = 1000,
  downstream = 1000,
  bin_size = 100,
  collapse_avg_fun = rowMeans,
  negate_neg_strand_values = FALSE,
  sample_name = NULL,
  group_name = NULL
)

Arguments

bw_plus	bigwig filename for plus strand signal
bw_minus	bigwig filename for minus strand signal
anno	Bed filename for annotations to use OR a GRanges object (see Details).
anchor	'TSS', 'TES', 'center' or NULL (default='TSS')
upstream	bp upstream of anchor (default=1000)
downstream	bp downstream of anchor (default=1000)
bin_size	size for binning in bp (default=1, ie no binning)
collapse_avg_fun	function for averaging values inside windows (Default = rowMeans, see Details).
negate_neg_strand_values	negate values from minus strand bigwig (default=FALSE).

Details

Loads the bed file. Extracts the position of the anchor point and creates ranges from x bp upstream to x bp downstream. Queries from both bigwigs and the correct strand. Summarizes signal of bin_size bins. negate_neg_strand_values can be set to TRUE to deal with minus strand bigwigs which contain all negative values as used by some labs. When using a GRanges object for anno, this assumes the bigwigs will be queries from start to end! All ranges must be exactly same size! anchor, upstream and downstream info is still reguired.

Value

Metagene object

Examples

bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")
bw_plus <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_plus_hg38.bw", package = "RMetaTools")
bw_minus <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_minus_hg38.bw", package = "RMetaTools")
anno=bedfile;anchor='center';upstream=1000;downstream=1000;window_size=10
collapse_fun = rowMeans;negate_neg_strand_values=FALSE
m <- metagene_rel_anchor(bw_plus, bw_minus, bedfile, anchor, upstream, downstream, window_size)
m

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