CRISPhieRmix: CRISPhieRmix

In timydaley/CRISPhieRmix: A tool for identifying interesting genes in large pooled CRISPRi and CRISPRa screen using hierarchical mixture models

Description

A tool for identifying interesting genes in large pooled CRISPRi and CRISPRa screen using hierarchical mixture models

a hierarchical mixture model for analysing large-scale CRISPRi/a pooled screen

Usage

CRISPhieRmix(x, geneIds, negCtrl = NULL, max_iter = 100, tol = 1e-10,
  pq = 0.1, mu = -4, sigma = 1, nMesh = 100, BIMODAL = FALSE,
  VERBOSE = FALSE, PLOT = FALSE, screenType = "GOF")

Arguments

x	log2 fold changes of guides targeting genes (required)
geneIds	gene ids corresponding to x (required)
negCtrl	log2 fold changes of negative control guides
max_iter	maximum number of iterations for EM algorithm, default = 100
tol	tolerance for convergence of EM algorithm, default = 1e-10
pq	initial value of p*q, default = 0.1
mu	initial value of mu for the interesting genes, default = -4
sigma	initial value of sigma for the interesting genes, default = 1
nMesh	the number of points to use in numerical integration of posterior probabilities, default = 100
BIMODAL	boolean variable to fit a bimodal alternative distribution for the case when both directions are of interest
VERBOSE	boolean variable for VERBOSE mode, default = FALSE
PLOT	boolean variable to produce plots, default = FALSE
screenType	acceptable options are "GOF" for gain of function screens (mu > 0) or "LOF" for loss of function screens, default = "LOF"

Value

a list containing genes, the corresponding posterior probabilities of being non-null, and the mixture fit

(return)

genes

vector of gene names

locfdr

posterior null probabilites of genes

genePosteriors

posterior non-null probabilities of genes

FDR

estimated global FDR of genes

mixFit

a list containing the estimated mixture fit

Author(s)

Timothy Daley, [e-mail]

Examples

Rosenbluh2017CRISPRi.sim.DESeq.log2fc.CRISPhieRmix =
CRISPhieRmix(x = Rosenbluh2017CRISPRiSim$x, geneIds = Rosenbluh2017CRISPRiSim$geneIds,
negCtrl = Rosenbluh2017CRISPRiSim$negCtrl, mu = -2, sigma = 0.5, nMesh = 200)

timydaley/CRISPhieRmix documentation built on July 13, 2019, midnight