Description Usage Arguments Value Author(s) See Also
To evaluate the overall accuracy, sensitivity, specificity, positive predictive value, negative predictive value.
1 2 | hlaCompareAllele(TrueHLA, PredHLA, allele.limit=NULL, call.threshold=NaN,
max.resolution="", output.individual=FALSE, verbose=TRUE)
|
TrueHLA |
an object of |
PredHLA |
an object of |
allele.limit |
a list of HLA alleles, the validation samples are
limited to those having HLA alleles in |
call.threshold |
the call threshold for posterior probability, i.e.,
call or no call is determined by whether |
max.resolution |
"2-digit", "4-digit", "6-digit", "8-digit", "allele", "protein", "2", "4", "6", "8", "full" or "": "allele" = "2-digit", "protein" = "4-digit", "full" and "" indicating no limit on resolution |
output.individual |
if TRUE, output accuracy for each individual |
verbose |
if TRUE, show information |
Return a list(overall, confusion, detail)
, or
list(overall, confusion, detail, individual)
if
output.individual=TRUE
.
overall
(data.frame):
total.num.ind |
the total number of individuals |
crt.num.ind |
the number of individuals with correct HLA types |
crt.num.haplo |
the number of chromosomes with correct HLA alleles |
acc.ind |
the proportion of individuals with correctly predicted HLA types (i.e., both of alleles are correct, the accuracy of an individual is 0 or 1.) |
acc.haplo |
the proportion of chromosomes with correctly predicted HLA alleles (i.e., the accuracy of an individual is 0, 0.5 or 1, since an individual has two alleles.) |
call.threshold |
call threshold, if it is |
n.call |
the number of individuals with call |
call.rate |
overall call rate |
confusion
(matrix): a confusion matrix.
detail
(data.frame):
allele |
HLA alleles |
train.num |
the number of training haplotypes |
train.freq |
the training haplotype frequencies |
valid.num |
the number of validation haplotypes |
valid.freq |
the validation haplotype frequencies |
call.rate |
the call rates for HLA alleles |
accuracy |
allele accuracy |
sensitivity |
sensitivity |
specificity |
specificity |
ppv |
positive predictive value |
npv |
negative predictive value |
miscall |
the most likely miss-called alleles |
miscall.prop |
the proportions of the most likely miss-called allele in all miss-called alleles |
individual
(data.frame):
sample.id |
sample id |
true.hla |
the true HLA type |
pred.hla |
the prediction of HLA type |
accuracy |
accuracy, 0, 0.5, or 1 |
Xiuwen Zheng
hlaAttrBagging
, predict.hlaAttrBagClass
,
hlaReport
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.