ascore: Alpha Score

In alexjgriffith/mulcal: To facilitate the analysis of multiple ChIP-Seq data sets

Description

Returns a seperating vector built from principle components. returns a matrix with a length of the data set inputed in heightFile and a width of the lenght of the number of options. As such a wide variety of seperating mechanisms can be called at the same time automating the process of isolating regions of data.

Usage

ascore(heightFile, pc, funs = rep("value", length(pc)), ns = rep(0,
  length(pc)), normMethod = "colQn")

Arguments

heightFile	Can be either a file name, a data.frame, or a matrix
pc	The principle component of interest, note the length of pc, funs and ns must be the same.
funs	funs=c("top","bottom","nottop","notbottom","middle","ranked","value")
ns	An integer to adjust the SD in the fun
normMethod	Default="colQn", use "non" if no normalization is desired

Value

An nxm matrix where n=length of data and m=number of optoins.

Author(s)

Alexander Griffith [e-mail]

Source

https://github.com/alexjgriffith/mulcal

See Also

For more infromation on callable functions ascoreSeperation

Examples

# load a bed file of format
# chr start end h1 ... hn
heightFile<-"some_bed_file.bed"

# loadHeightFile splits the first three columns into
# stats and the remainder into data
# You can use any utiltity you wish to load data so
# long as it clearly seperates the data (heights, read pile up,
# etc) from the stats (chromosome inforomation, data source, genes etc)
values<-loadHeightFile(heightFile)
data<-values$data
stats<-values$stats

pc<-1
function<-"top" # x>mean+sd*n
n<-3
reg<-ascore(data,pc,function,n)
stats[reg]

# Determining two values at the same time
reg2<-ascore(data,c(1,2),c("top","top"),c(3,1))
regions<-apply(reg2,1,all)
stats[regions]

# Saving the first 3 principle components
pcs<-ascore(data,c(1,2,3,4))

reg4<-ascoreSeperation(pcs[1,],"top",3)

alexjgriffith/mulcal documentation built on May 10, 2019, 8:53 a.m.