makeSplines {Starr} | R Documentation

## Fit splines to profiles

### Description

This function uses the pspline package to fit spilnes to each entry in a list of profiles.

### Usage

    makeSplines(profiles, df=1000)

### Arguments

`profiles` | a list as it is created by the getProfiles package.
`df` | the degree of freedom of the fit

### Value

a list as it is created by the getProfiles function.

### Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

### See Also

`smooth.Pspline`, `predict.smooth.Pspline`

### Examples

    ##
    # dataPath <- system.file("extdata", package="Starr")
    # bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))

    # cels <- c(file.path(dataPath,"Rpb3_IP_chr1.cel"), file.path(dataPath,"wt_IP_chr1.cel"),
    # 	file.path(dataPath,"Rpb3_IP2_chr1.cel"))
    # names <- c("rpb3_1", "wt_1","rpb3_2")
    # type <- c("IP", "CONTROL", "IP")
    # rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData=TRUE, log.it=TRUE)

    # ips <- rpb3Chr1$type == "IP"
    # controls <- rpb3Chr1$type == "CONTROL"

    # rpb3_rankpercentile <- normalize.Probes(rpb3Chr1, method="rankpercentile")
    # description <- c("Rpb3vsWT")
    # rpb3_rankpercentile_ratio <- getRatio(rpb3_rankpercentile, ips, controls, description, fkt=median, featureData=FALSE)

    # probeAnnoChr1 <- bpmapToProbeAnno(bpmapChr1)
    # transcriptAnno <- read.gffAnno(file.path(dataPath, "transcriptAnno.gff"), feature="transcript")

    # profile <- getProfiles(rpb3_rankpercentile_ratio, probeAnnoChr1, transcriptAnno, 500, 500, feature="transcript", borderNames=c("TSS", "TTS"), method="basewise", sameLength=T, fill=T, distance=8, spacing=4)
    # profile_splines <- makeSplines(profile)

[Package Starr version 1.38.0 Index]