get_matrix: Metagene Matrix
In manschmi/RMetaTools: Tools For Metagene Analysis

Description Usage Arguments Details Value Examples

Creates metagene matrix for both strands using 1 or 2 bigwig files.

get_matrix(
  bw_plus,
  bw_minus,
  anno,
  upstream = 1000,
  downstream = 1000,
  collapse_to_win_size = NULL,
  collapse_to_n_wins = NULL,
  collapse_avg_fun = rowMeans,
  negate_neg_strand_values = FALSE
)

`bw_plus`	filename for plus strand bigwig file.
`bw_minus`	filename for minus strand bigwig file.
`anno`	GRanges object of regions to query.
`upstream`	bp upstream of anchor (default=1000)
`downstream`	bp downstream of anchor (default=1000)
`collapse_to_win_size`	size for binning in bp (default=1, ie no binning)
`collapse_to_n_wins`	number of bins to collapse to (default=NULL, 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).

Loads the bed file. Anchored mode requires a anchor, upstream and downstream, extracts the position of the anchor point and creates ranges from x bp upstream to x bp downstream. I anchor, upstream and downstream are NULL, collects values over specified entire regions. If collapse_to_win_size is set to a integer > 0, uses collapse_avg_fun (rowMeans, rowSums or similar) to overage signals within this range See collapse_to_window_size for more info about averaging over window size. If collapse_to_n_wins is not NULL, ups: this requires collapse_avg_fun to be set to mean, sum or similar (ie instead of the default rowMeans) to overage signals into x equally sized bins. Only used if collapse_to_win_size is not > 1. See collapse_to_n_windows for more info about averaging into defined number of windows. 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.

matrix with columns from most upstream to most downstream and rows are the individual regions. Rownames are the Name column from the bed file.

bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")
regions <- meta_regions(bedfile, 'TSS', 1000, 5000)
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")
mat <- get_matrix(bw_plus, bw_minus, regions, 1000, 5000, 1)
dim(mat)
mat <- get_matrix(bw_plus, bw_minus, regions, 1000, 5000, 50)
dim(mat)
mat <- get_matrix(bw_plus, bw_minus, regions, 1000, 5000, collapse_to_n_wins=5, collapse_avg_fun=mean)
dim(mat)

#if bigwigs are not stranded, ie from ChIP experiment both plus and minus are the same file
bw <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_hg38.bw", package = "RMetaTools")
mat <- get_matrix(bw, bw, regions, 1000, 5000, 50)