setIntervalScale: Set x and y interval of the HTCexp object

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/binningC.R

Description

Set x and y interval of the HTCexp object and update the contact map accordingly

Usage

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setIntervalScale(x, xgi, ygi, upa=TRUE, method=c("sum","median","mean"),
use.zero=TRUE, optimize.by = c("speed", "memory"))

Arguments

x

object that inherits from class HTCexp

ygi

y intervals; see class GRanges for details

xgi

x intervals; see class GRanges for details

upa

logical; unique primer assignment. Allow one primer to belong to one or several bins

method

the method used to combine the counts. Must be ‘mean’, ‘median’ or ‘sum’

use.zero

logical; use the zero values in the method calculation

optimize.by

"speed" will use faster methods but more RAM, and "memory" will be slower, but require less RAM

Details

Define new contact map based on the specified xgi and ygi intervals.

This function has to be used carefully and can has important impact on the contact map. It is important to note that the setIntervalScale function is different from the binningC function in the way that the output is not symetrical.

Value

A HTCexp object

Author(s)

N. Servant

See Also

HTCexp-class

Examples

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data(Nora_5C)

E14.bin<-binningC(E14$chrXchrX)

## I have two HTCexp samples defined with different intervals.
show(E14.bin)
show(MEF$chrXchrX)

## How to compare them ?
## One idea is to force the intervals definition of one object using the
## intervals of the other.

setIntervalScale(MEF$chrXchrX, xgi=x_intervals(E14.bin), ygi=y_intervals(E14.bin))

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.