hlaReport: Format a report

In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description

Create a report for evaluating prediction accuracies.

Usage

hlaReport(object, export.fn="", type=c("txt", "tex", "html", "markdown"),
    header=TRUE)

Arguments

object	an object returned by hlaCompareAllele
export.fn	a file name for output, or "" for stdout
type	"txt" – tab-delimited text format; "tex" – tex format using the 'longtable' package; "html" – html file
header	if TRUE, output the header of text file associated corresponding format

Value

None.

Author(s)

Xiuwen Zheng

See Also

hlaCompareAllele

Examples

# make a "hlaAlleleClass" object
hla.id <- "A"
hla <- hlaAllele(HLA_Type_Table$sample.id,
    H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
    H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
    locus=hla.id, assembly="hg19")

# divide HLA types randomly
set.seed(100)
hlatab <- hlaSplitAllele(hla, train.prop=0.5)
names(hlatab)
# "training"   "validation"
summary(hlatab$training)
summary(hlatab$validation)

# SNP predictors within the flanking region on each side
region <- 500   # kb
snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position,
    hla.id, region*1000, assembly="hg19")
length(snpid)  # 275

# training and validation genotypes
train.geno <- hlaGenoSubset(HapMap_CEU_Geno,
    snp.sel = match(snpid, HapMap_CEU_Geno$snp.id),
    samp.sel = match(hlatab$training$value$sample.id,
    HapMap_CEU_Geno$sample.id))
test.geno <- hlaGenoSubset(HapMap_CEU_Geno,
    samp.sel=match(hlatab$validation$value$sample.id,
    HapMap_CEU_Geno$sample.id))

# train a HIBAG model
set.seed(100)
# please use "nclassifier=100" when you use HIBAG for real data
model <- hlaAttrBagging(hlatab$training, train.geno, nclassifier=4,
    verbose.detail=TRUE)
summary(model)

# validation
pred <- hlaPredict(model, test.geno)
# compare
(comp <- hlaCompareAllele(hlatab$validation, pred, allele.limit=model,
    call.threshold=0))


# report
hlaReport(comp, type="txt")

hlaReport(comp, type="tex")

hlaReport(comp, type="html")

hlaReport(comp, type="markdown")

HIBAG documentation built on March 24, 2021, 6 p.m.