DerivData-class: Class "DerivData"

In CNAnorm: A normalization method for Copy Number Aberration in cancer samples

Description

A Class containing data derived from InData used for further computation and plotting.

Objects from the Class

Objects can be created by calls of the form new("DerivData"), however DerivData is typically populated using methods. If a slot has not been populated yet, it has zero length, otherwise slots have the same length as InData.

Slots

ratio:

Numeric vector with ratio Test/Normal. Optionally GC corrected.

ratio.s:

Numeric vector with smoothed ratio.

ratio.n:

Numeric vector with normalized ratio.

ratio.s.n:

Numeric vector with normalized and smoothed ratio.

segID:

Numeric vecotr with ID of segmented data (as provided by DNACopy). Each segment has a different ID.

segMean:

Numeric vector with mean value of the segment (as provided by DNACopy.)

segMean.n:

Numeric vector with normalized segMean.

ok4density:

Logical vector. Specify wich values have been used to calculate density.

Methods

length

signature(x = "DerivData"): Returns number of windows.

Author(s)

Stefano Berri and Arief Gusnanto

References

Gusnanto, A., Wood, H.M., Pawitan, Y., Rabbitts, P. and Berri, S. (2011) Correcting for cancer genome size and tumor cell content enables better estimation of copy number alterations from next generation sequence data. Bioinformatics

See Also

CNAnorm, InData-class

Examples

data(LS041)
inObject <- new("InData", Chr = as.character(LS041$Chr), 
    Pos = LS041$Pos, Test = LS041$Test, Norm = LS041$Norm, 
    GC = LS041$GC)
CNA <- new("CNAnorm", InData = inObject) 

CNAnorm documentation built on Nov. 8, 2020, 5:29 p.m.