readSdrf {wrProteo}

Read proteomics meta-data as sdrf file

Description

This function allows reading proteomics meta-data from sdrf file, as they are provided on https://github.com/bigbio/proteomics-sample-metadata. A data.frame containing all annotation data will be returned. To stay conform with the (non-obligatory) recommendations, columnnames are shown as lower caps.

Usage

readSdrf(
  fi,
  chCol = "auto",
  urlPrefix = "github",
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

fi

(character) main input; may be full path or url to the file with meta-annotation. If a short project-name is given, it will be searched based at the location of urlPrefix

chCol

(character, length=1) optional checking of column-names

urlPrefix

(character, length=1) prefix to add to search when no complete path or url is given on fi, defaults to proteomics-metadata-standard on github

silent

(logical) suppress messages

callFrom

(character) allows easier tracking of messages produced

debug

(logical) display additional messages for debugging

Details

The packages utils and wrMisc must be installed. Please note that reading sdrf files (if not provided as local copy) will take a few seconds, depending on the responsiveness of github. This function only handles the main reading of sdrf data and some diagnostic checks. For mining sdrf data please look at replicateStructure and readSampleMetaData.

Value

This function returns the content of sdrf-file as data.frame (or NULL if the corresponding file was not found)

See Also

readSampleMetaData, replicateStructure,

Examples

## This may take a few sconds...
sdrf001819 <- readSdrf("PXD001819")
str(sdrf001819)