Collect samples fulfilling the specified requirements

This funciton collects the samples from a data.table-class object that fulfill the requirements of an attribute attr specified with the fun argument

fetchSamples(samples, attr = NULL, func = NULL, action = "include")

Arguments

samples: an object of data.table-class class
attr: a string specifying a column in the samples
func: an anonymous function, see Details for more information
action: a string (either include or exclude) that specifies whether the function should select the row or exclude it.

Value

an object of data.table-class class filtered according to specified requirements

Details

The anonymous function provided in the func argument has to return an integer that indicate the rows that the action should be performed on. Core expressions which are most useful to implement the anonymous function are:

which with inequality signs: ==,>,<
grep

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
p = Project(projectConfig)
#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
#>   amendments: newLib,newLib2
s = sampleTable(p)
fetchSamples(s,attr = "sample_name", func=function(x){ which(x=="pig_0h") },action="include")
#>    sample_name protocol organism time                      file_path
#> 1:      pig_0h     RRBS      pig    0 /data/lab/project/pig_0h.fastq
fetchSamples(s,attr = "sample_name", func=function(x){ which(x=="pig_0h") },action="exclude")
#> Empty data.table (0 rows and 5 cols): sample_name,protocol,organism,time,file_path
fetchSamples(s,attr = "sample_name", func=function(x){ grep("pig_",x) },action="include")
#>    sample_name protocol organism time                      file_path
#> 1:      pig_0h     RRBS      pig    0 /data/lab/project/pig_0h.fastq
#> 2:      pig_1h     RRBS      pig    1 /data/lab/project/pig_1h.fastq