Xpert Parsing R6

The class used to parse Xpert HPV results

Methods

Public methods

• Xpert$new()

• Xpert$getResults()

• Xpert$getPDFs()

• Xpert$clone()

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Method new()

Parse new pdf of xpert result(s)

Usage

Xpert$new(pdf, xpertTZ = Sys.timezone())

Arguments

pdf

path to pdf or raw vector of pdf. The pdf may contain a single or multiple results. Only one pdf can be specified in the path

xpertTZ

timezone of xpert machine (see OlsonNames()) or TZ R6 object of machine mapped timezimes

Returns

a Xpert R6 Object

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Method getResults()

Get xpert_result (a data.frame) for a particular index

Usage

Xpert$getResults(idx)

Arguments

idx

integer vector of indices of xpert results to return, if not provided, function will return all parsed results

Returns

a xpert_result class (a specialized data.frame)

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Method getPDFs()

Write the single xpert result pdf to disk

Usage

Xpert$getPDFs(idx, output)

Arguments

idx

single integer of results parsed in this class

output

path to output pdf (you must specify extension .pdf yourself). If not provided will create a file named using sample_id in a temp directory

Returns

the path of the saved pdf

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Method clone()

The objects of this class are cloneable with this method.

Usage

Xpert$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.