hpaXmlTissueExpr: Extract tissue expression details

In anhtr/HPAanalyze: Retrieve and analyze data from the Human Protein Atlas

Extract tissue expression details

Description

Extract tissue expression information for each sample and url to download images from imported xml document resulted from hpaXmlGet(). It is important to note that the data that HPA provides on their website and through xml files are not one-to-one equivalents. For example, xml files usually only provide one of the two histology image for each patient.

Usage

hpaXmlTissueExpr(importedXml)

Arguments

importedXml

Input an xml document object resulted from a hpaXmlGet() call.

Value

This function returns a list of tibbles, each for an antibody. Each tibble contains information about all individual samples and their staining. Due to the variation in amount of information available for these samples, the number of columns differs, but the tibble essentially includes: patientId, age, sex, staining, intensity, quantity, location, imageUrl, snomedCode, and tissueDescription. The last two items may have more than one column each.

See Also

Other xml functions: hpaXmlAntibody(), hpaXmlGet(), hpaXmlProtClass(), hpaXmlTissueExprSum(), hpaXml()

Examples

## Not run: 
  GCH1xml <- hpaXmlGet('ENSG00000131979')
  hpaXmlTissueExpr(GCH1xml)

## End(Not run)

anhtr/HPAanalyze documentation built on June 3, 2023, 2:19 a.m.