R: CNV.fit

CNV.fit {conumee}

R Documentation

CNV.fit

Description

Normalize query sample intensities by fitting intensities to reference set using a linear regression model.

Usage

CNV.fit(query, ref, anno, ...)

## S4 method for signature 'CNV.data,CNV.data,CNV.anno'
CNV.fit(query, ref, anno, name = NULL,
  intercept = TRUE)

Arguments

`query`	`CNV.data` object of query sample (single sample).
`ref`	`CNV.data` object of reference set.
`anno`	`CNV.anno` object. Use `CNV.create_anno` do create.
`...`	Additional parameters (`CNV.fit` generic, currently not used).
`name`	character. Optional parameter to set query sample name.
`intercept`	logical. Should intercept be considered? Defaults to `TRUE`.

Details

The log2 ratio of query intensities versus a linear combination of reference set intensities that best reflects query intensities is calculated (as determined by linear regression). The annotations provided to CNV.fit are saved within the returned CNV.analysis object and used for subsequent analysis steps.

Value

CNV.analysis object.

Author(s)

Volker Hovestadt conumee@hovestadt.bio

Examples

# prepare
library(minfiData)
data(MsetEx)
d <- CNV.load(MsetEx)
data(detail_regions)
anno <- CNV.create_anno(detail_regions = detail_regions)

# create object
x <- CNV.fit(query = d['GroupB_1'], ref = d[c('GroupA_1', 'GroupA_2', 'GroupA_3')], anno)

# modify object
#x <- CNV.bin(x)
#x <- CNV.detail(x)
#x <- CNV.segment(x)

# general information
x
show(x)

# coefficients of linear regression
coef(x)

# show or replace sample name
names(x)
names(x) <- 'Sample 1'

[Package conumee version 1.13.0 Index]