CellMix 1.6

Condition Number of a Marker List

Description

The S3 method kappa for MarkerList objects returns the condition number of a data (sub-)matrix limited to markers in the list.

Usage

S3 (MarkerList)
`kappa`(z, data, n = 0, ...)

Arguments

z
a MarkerList-class object
data
reference data matrix or ExpressionSet object, from which is extracted the sub-matrix of markers.
n
specifies the range of total number of markers that compose the matrix whose condition number is computed:
  • The default (0) is to compute using all makers in z that can be found in the data.
  • A single positive value indicates the exact number of such markers to use. A warning is thrown if this number is greater than the number of markers present in the data.
  • A single negative value does the same as a positive value, but no warning is thrown if it exceeds the actual number of markers in the data.
  • NULL indicates a full range of number of markers, i.e. the computation is performed including for matrices composed of length(z) to n markers.
  • A numeric vector completely specifies the range of number of markers over which to perform the computation.
...
extra arguments passed to kappa.

Details

This method typically is used to predict/optimise the deconvolution power of a set of cell-specific signatures, as proposed by Abbas et al. (2009).

References

Abbas AR, Wolslegel K, Seshasayee D, Modrusan Z and Clark HF (2009). "Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus." _PloS one_, *4*(7), pp. e6098. ISSN 1932-6203, , .

Examples


# random data and markers
d <- rmatrix(20, 10)
x <- rMarkerList(4, 5)
summary(x)

##       Length Class  Mode   
## Type1 5      -none- numeric
## Type2 5      -none- numeric
## Type3 5      -none- numeric
## Type4 5      -none- numeric

kappa(x, d)

## [1] 13.69


# over a specifc or range of total number of markers
kappa(x, d, 6)

##     6 
## 9.193

kappa(x, d, 1:20)

##      4      5      6      7      8      9     10     11     12     13 
##  8.129  9.129  9.193  9.305 11.843 18.388 81.702 41.196 39.737 40.317 
##     14     15     16     17     18     19     20 
## 28.722 16.100 14.131 13.093 13.910 14.172 13.688 
## attr(,"mins")
##     4 
## 8.129 
## attr(,"n")
## [1] 4


# condition number is Inf if no markers are found
# NB: throws a warning
rownames(d) <- as.character(1:nrow(d))
x <- rMarkerList(4, 5, names=TRUE)
kappa(x, d)

## Warning: Could not find any markers in data

## [1] Inf

See also

kappa