CNV.fit {conumee} | R Documentation |
Normalize query sample intensities by fitting intensities to reference set using a linear regression model.
CNV.fit(query, ref, anno, ...) ## S4 method for signature 'CNV.data,CNV.data,CNV.anno' CNV.fit(query, ref, anno, name = NULL, intercept = TRUE)
query |
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ref |
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anno |
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... |
Additional parameters ( |
name |
character. Optional parameter to set query sample name. |
intercept |
logical. Should intercept be considered? Defaults to |
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.
CNV.analysis
object.
Volker Hovestadt conumee@hovestadt.bio
# 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'