read_samplesheets: Read sample sheet information from Illumina sequencing run(s)
In eriqande/microhaplotopia: Tools for Working with Microhaplot Data a la the SWFSC

This function is designed to identify all summary data files within a folder and join them together in R for further data processing. A single file or an entire folder of data files can be read and joined with this function. If a subset of files within a folder is desired, the user should supply the function with a list of file paths.

1	read_samplesheets(datapath, n_skip)

datapath

path to Illumina Sample sheet files that are loaded onto sequencers for demultiplexing. If this is a directory, then all the files within it ending with .csv or .csv.gz will be processed. If datapath is single file with a csv extension then only that file will be loaded. If it is a vector of file paths, at least one of which has a .csv or a .csv.gz extension, then the function will attempt to load all of the files.

n_skip

is the number of lines to skip. The sample sheets loaded onto Illumina sequencing machines have a header of 'n_skip' lines above the useful metadata. Open one of the SampleSheet files that is in your datapath folder and identify the appropriate number of lines to skip. The first line read should be column names of the metadata. For example at the NOAA SWFSC the first columns of metadata are: Sample_ID, Sample_Name, Sample_Plate...etc.

eriqande/microhaplotopia documentation built on July 7, 2020, 1:16 a.m.