subtypes,PAM50-method {pbcmc} | R Documentation |
subtypes
for PAM50 adaptation with permuted results.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:
all subtype have fdr > pcutoff. Hence, there is evidence that the observed ρ can be obtained by random chance.
only one fdr <= pcutoff. There is not enough evidence to say that the observed ρ does not belong to the null distribution.
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.
If the statement is TRUE.
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.
## S4 method for signature 'PAM50' subtypes(object, pCutoff = 0.01, corCutoff = 0.1, where = c("fdr", "pvalue")[1])
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". |
a PAM50 object with the updated slots:
@permutation |
. |
@parameters |
$pCutoff, $corCutoff and $where are updated accordingly. |
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
Perou CM, Sorlie T, Eisen MB, et al., 2000, Molecular portraits of human breast tumors. Nature 406:747-752.
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.
PAM50
for a complete example.
Other PAM50: as
,
classify,PAM50-method
,
filtrate,PAM50-method
,
pam50centroids
,
permutate,PAM50-method
,
subjectReport,PAM50-method
##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