subtypes,PAM50-method {pbcmc} | R Documentation

## Subject `subtypes` for PAM50 adaptation with permuted results.

### Description

PAM50 subtypes are obtained using permuted test results. The idea is to give confidence in PAM50 subtype assessment (Perou et al. 2000 & 2010). In this context, the observed Spearman's ρ correlation is tested against the null distribution obtained for each subtype. Then, only significant correlations are used in according to the following scheme:

Not assigned

  all subtype have fdr > pcutoff. Hence, there is evidence that the observed ρ can be obtained by random chance.

Assigned

  only one fdr <= pcutoff. There is not enough evidence to say that the observed ρ does not belong to the null distribution.

Ambiguous

  more than one have fdr <= pcutoff. Then, one of the following alternatives holds given the result of |ρ(profile, class_A)-ρ(profile, class_B)|>corCutoff.

  Assigned

    If the statement is TRUE.

  Ambiguous

    If the statement is FALSE.

Under the above scheme, the physician has an objective measurement to support the patient treatment decision. Both, with the given permuted subtype and by interpreting the p-value or fdr of each subtype null distribution test.

### Usage

    ## S4 method for signature 'PAM50'
    subtypes(object, pCutoff = 0.01, corCutoff = 0.1,
        where = c("fdr", "pvalue")[1])

### Arguments

`object` | a MolecularPermutationClassifier subclass object.
`pCutoff` | numeric with p-value/fdr cutoff used depending on "where" selection. Default: 0.01.
`corCutoff` | numeric with correlation difference between classes cutoff used, i.e., |ρ(profile, class_A)-ρ(profile, class_B)|>corCutoff. Default 0.1
`where` | character with significant value used. Default value is "fdr".

### Value

a PAM50 object with the updated slots:

`@permutation` | $subtype data.frame with the following fields $PAM50 the original PAM50 subtype $Permuted factor with the following levels: "Not assigned": all subtype have fdr > pcutoff "Assigned": only one fdr <= pcutoff "Ambiguous": more than one fdr <= pcutoff $Classes a character according to "Permuted" field: the unique PAM50 subtype if "Assigned" a combination for "Ambiguous" or NA if "Not assigned". $Class idem as Classes but "Ambiguous" is set to PAM50 calls $Subtype Classes but "Ambiguous" is kept as "Ambiguous" string .
`@parameters` | $pCutoff, $corCutoff and $where are updated accordingly.

### Author(s)

Cristobal Fresno cfresno@bdmg.com.ar, German A. Gonzalez ggonzalez@bdmg.com.ar, Andrea S. Llera allera@leloir.org.ar and Elmer Andres Fernandez efernandez@bdmg.com.ar

### References

1. Perou CM, Sorlie T, Eisen MB, et al., 2000, Molecular portraits of human breast tumors. Nature 406:747-752.

2. Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PB., 2010, Clinical implementation of the intrinsic subtypes of breast cancer, The Lancet Oncology 11(8):718-719.

### See Also

`PAM50` for a complete example.

Other PAM50: `as`, `classify,PAM50-method`, `filtrate,PAM50-method`, `pam50centroids`, `permutate,PAM50-method`, `subjectReport,PAM50-method`

### Examples

    ##Using pam50centroids package example data, which already had been
    ##filtrated, classified and permutated.
    data(pam50centroids)
    summary(pam50centroids)

    ##Now, let's change pCutoff and corCutoff without the need to run pemutate
    ##again
    pam50centroids<-subtypes(pam50centroids, pCutoff=0.01, corCutoff=Inf,
        where="fdr")
    pam50centroids
    summary(pam50centroids)##Note that only Basal is not Ambiguos

[Package pbcmc version 1.8.0 Index]