ngsFormatDF: Format NGS data frame
In EricArcher/swfscGenetics: Miscellaneous functions for genetic data manipulation

Description Usage Arguments Author(s) See Also

View source: R/ngsFormatDF.R

Format NGS data frame for accessioning. Assigns correct column names, checks that files found.

ngsFormatDF(
  library.name,
  library.filename = NULL,
  labid = "LABID",
  d.id = "D_id",
  species = "species",
  i7.index = "i7_index",
  i5.index = "i5_index",
  read.direction = "Read_direction",
  library.directory = "Library_Directory",
  original.filename = "Original_Filename",
  comments = "Comments"
)

`library.name`	name of run library. This should also be the folder name where the files to be archived are located.
`library.filename`	filename of library spreadsheet. If `NULL`, the .csv file in the `library.name` folder
`labid`	SWFSC LABID column name
`d.id`	DNA ID column name (optional)
`species`	species name column name
`i7.index`	forward index column name
`i5.index`	reverse index column name
`read.direction`	direction of reads column name
`library.directory`	original folder of file within the run folder specified by `library.name` (optional)
`original.filename`	original filename of `.fastq.gz` file (optional). If the column does not exist, or values are empty for a row, the function will look for a file beginning with '`<labid>_`' and has '`<read.direction>_`' somewhere in the filename
`comments`	any text comments about the record (optional)