gcq: gcq

Description Usage Arguments Details Examples

View source: R/gcq.R

Description

This function is for calculating GC content in CRISPR/Cas9 deletions that have already been analysed using the mhq function. It filters the deletions for those with a given amount of microhomology and then performs a chi sqaure test to compare the observed vs the expected GC content of the microhomologies.

Usage

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gcq(input, MH, equalTo = F, expected, CRISPResso = T)

Arguments

input

dataframe output after running mhq(yourData)

MH

microhomology amount to filter for

equalTo

if set to TRUE search ONLY for microhomologies equal to MH. If set to FALSE search for microhomologies greater than or equal to MH

expected

background GC content over the region containing deletions (if 50 percent background, expected=0.5.) Determined by the user.

CRISPResso

are you analysing a dataframe containing analysed CRISPResso data?

Details


Output is a dataframe with columns:

Examples

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gcq(mhqOutCRISPResso, MH=1, equalTo=F, expected=0.46, CRISPResso=T)
gcq(mhqOutSanger, MH=2, equalTo=T, expected=0.51, CRISPResso=F)

d0minicO/mhscanR documentation built on May 4, 2021, 5:22 p.m.