crosshyb_func {crosshybDetector} | R Documentation |
It is usually called from within crosshyb
, but can be invoked directly.
The algorithm is described into the paper in References
section
crosshyb_func(input, seqList, mysub, numPermut, probes, satValue, maxProbes, delta = 10)
input |
A dataframe containing the i) raw intensity value, ii) the probe type (e.g. spike, probes, negative,...) and iii) the probe name |
seqList |
An object of class AASequenceList created with readFasta |
mysub |
Substitution matrix to be used for the alignment |
numPermut |
Number of permutations for Monte Carlo simulations |
probes |
A vector with the probes to be analyzed (e.g. probes, spike, etc) |
satValue |
The value corresponding to saturated probes |
maxProbes |
The maximun number of probes to analyze |
delta |
Threshold for difference in melting temperature. Pairs of probes whose delta Tm
is lower than delta are considered as similar. Delta Tm i,k is computed as Tm i,i - Tm i,k,
where Tm i,i is the Tm of the percect pairing probe i vs probe i and Tm i,k is the Tm of the
imperfect pairing probe i vs probe k
|
A list containing:
data |
Dataframe with three columns containing the results of the analysis for the putative corruptor probes. Contains: i) the probe number, ii) the probe name and iii) the pvalue based on Monte Carlo simulations of being a corruptor (pvalue is corrected for multiple testing) |
children |
A list containing the corrupted probes for each putative corruptor |
Paolo Uva
Uva, P., and de Rinaldis, E. CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments. BMC Bioinformatics 2008, 9:485