annotationTable: Extract facts from an Annotation Table

Description Usage Arguments Details Value Author(s) See Also

Description

Functions to query an Annotation Table for keyed values about one or more named sample datasets.

Usage

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readAnnotationTable(file, neededColumns = NULL, sep = "\t", verbose = FALSE)
getAnnotationValue(tbl, key, columnArg, notfound = "", verbose = TRUE)
getAnnotationTrue(tbl, key, columnArg, notfound = FALSE, verbose = TRUE)
whichAnnotationTrue(tbl, columnArg, negate = FALSE, verbose = TRUE)

Arguments

file

Name of a sample annotation file.

neededColumns

Optional character vector of required column names that the annotation table must contain.

tbl

Either an annotation table previously read via 'readAnnotationTable' or a character string file name to open and read from.

key

The keyword value that determines which one row the the annotation to query. This is required to be an entry in the first (leftmost) column of the annotation table.

columnArg

The name of one column in the annotation table being queried.

notfound

The value to be used if that column is not found in the annotation table.

negate

Should the column of logical values be negated before evaluating 'which'.

verbose

report the details of the search

Details

This is the principal means of querying sample specific values that affect the runtime behavior of many Duffy Lab package tools. For settings that are not sample specific, see OptionsTable.

The annotation table is a text file with tab separated fields. Each row represents one sample or dataset or experiment, where the first (leftmost) column is typically labeled 'SampleID' and that column is the sample identifier. The file may include a column called 'Include' or 'Exclude' that controls which rows of the table are actually read in from the file. This makes it easy to control what subset of samples are seen by the analysis tools.

Any text in the annotation table file can have embedded environment variables, which will be run-time substituted at the time they are 'gotten'.

The truth of a value uses the general heuristic that F, False, N, No, 0, and the empty string "" resolve to FALSE and everything else is TRUE. See as.TRUEorFALSE.

Value

For readAnnotationTable a table of sample annotation values, with 'excluded' rows removed.

For getAnnotationValue the one entry from the table at: row='key', col='arg' as a characer string, or the 'notfound' value.

For getAnnotationTrue the one entry from the table at: row='key', col='arg' as a logical value, or the 'notfound' value.

For whichAnnotationTrue a vector of row numbers where column 'arg' resolves to a logical TRUE value, after possible negation.

Author(s)

Bob Morrison

See Also

readOptionsTable, getOptionValue, getOptionTrue, for corresponding functions for program options that are not sample specific.


robertdouglasmorrison/DuffyTools documentation built on Dec. 7, 2018, 8:02 a.m.