genewise: Genewise screening

In ybai3/SCQC: Single Cell Sequencing Data Quality Control

Description

Gene-wise screening is based on the expectation that for a gene with a low technical noise, a gene<e2><80><99>s count in a library will tend to increase with the increase of library size, which was tested using negative binomial regression of gene count (as dependent variable) against library size (as independent variable). We kept only those genes achieving a significant (FDR>0.10), positive regression coefficient.

Usage

genewise(x,presetfdr=0.1)

Arguments

submatrix	housekeeping or non-housekeeping countmatrix from previous step
presetfdr	preset false discovery rate

Value

a list contaitning

beta_nb	the beta values of negative binomial regression
beta_cleaned	beta values controlled by FDR
fdr	Flase discovery rate for each gene
countmatrix_rwcl	genewise cleaned countmatrix

Examples

genewise(matrix,presetfdr=0.15)


{ genewise }

ybai3/SCQC documentation built on May 19, 2019, 9:40 p.m.