connInteger: Create a conns files and then analyzes them

Description Usage Arguments Value Examples

View source: R/connInteger.R

Description

Takes in a cds files and turns them into conns files and then analyzes them with an integer weighting

Usage

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connInteger(WT_cicero_cds, KO_cicero_cds, vector, mm10.chr, namefirst,
  namesecond, thresh, changePerc, viablethresh)

Arguments

WT_cicero_cds

the first cds you want to convert to a conns file

KO_cicero_cds

the second cds you want to convert to a conns file

vector

the vector containing which chromosones you are interested in

mm10.chr

the genome file you are referencing to create the conns files

namefirst

the label you want to give to the first conns file, i.e. "A"

namesecond

the label you want to give to the second conns file, i.e. "B"

thresh

the threshold for peaks you are interested in

changePerc

the percent difference between Ko and WT conns you want to use as a threshold

viablethresh

the threshold for peaks you consider viable

Value

a completed, sorted, and eleaborated dataframe

Examples

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SUM.data = connWeight(WT_cicero_cds, KO_cicero_cds, vector, mm10.chr, namefirst, namesecond, thresh, changPerc)

samissimas/ciceroAddition documentation built on Aug. 10, 2019, 12:02 a.m.