batch_housekeep: Found housekeep genes in batch effects group

In wangjiaxuan666/fixbatch: The goal of packages is fixing the batch effect in data

Found housekeep genes in batch effects group

Description

batch_housekeep allows users to Found housekeep genes in batch effects group by coefficient of variation and the expression sum.

Usage

batch_housekeep(
  data,
  batch = NULL,
  expcv = 1,
  exphigh = 1,
  explow = 0,
  housekeep_gene = NULL
)

Arguments

data	Genomic measure matrix (dimensions probe x sample) - for example, expression matrix
batch	must be a vctor,Batch covariate (only one batch allowed)
expcv	a number range 0 to 1, Sets the maximum quantile value of the coefficient of variation
exphigh	a number range 0 to 1, Sets the maximum quantile value of expression sum
explow	a number range 0 to 1, Sets the minimum quantile value of expression sum
housekeep_gene	This is a very difficult word to spell, so that you can think carefully when you use it. the input must be a vector and including by the rownames of input data

Value

data A housekeep gene x sample genomic measure matrix

Examples

y <- matrix( rpois(1200, lambda=6), nrow=200 )
n = dim(y)
colnames(y) = paste(rep("sample",n[[2]]),1:n[[2]])
rownames(y) = paste(rep("gene",n[[1]]),1:n[[1]])
y = as.data.frame(y)
y[3,] <- c(0,0,0,1,1,1)
y[19,] <- c(1,0,1,0,1,0)
data = y
batch = rep(1:2, each = 3)
#re = batch_housekeep(data, bacth, expcv = 1, exphigh, explow = 0)
#re1 = batch_housekeep(data,batch,housekeep_gene = c(paste(rep("gene",3),c(6:9,2000))))

wangjiaxuan666/fixbatch documentation built on Jan. 25, 2024, 4:39 p.m.