lpe.var: A function evaluating LPE variance of data with replicates

In JungsooGIM/LPEseq: LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates

Description

A function evaluating LPE variance of data with replicates

Usage

lpe.var(y, n.bin = n.bin, df = df)

Arguments

y	gene expressino whose variance to be estimated
n.bin	the number of bins
df	degree of freedom in smoothing (arg of smooth.spline())

Details

See the reference paper. See also Jain et al. (2003) Bioinformatics.

Value

matrix

evaluated LPE

Author(s)

Jungsoo Gim

References

J. Gim and T. Park, PLoS ONE under revision (http://bibs.snu.ac.kr/software/LPEseq)

Examples

## Generating a replicated simulation dataset
simData <- generateData(n.deg=1000)

## Normalization
normData <- generateData(simData[,-7])

## Evaluating lpe object for each condition with replicates
lpe.x <- lpe.var(normData[,1:3], n.bin=100, df=10)
lpe.y <- lpe.var(normData[,4:6], n.bin=100, df=10)

JungsooGIM/LPEseq documentation built on May 16, 2019, 10:04 a.m.