import_Vispa2_stats {ISAnalytics} | R Documentation |
Imports all the Vispa2 stats files for each pool provided the association
file has been aligned with the file system
(see
import_association_file
).
import_Vispa2_stats( association_file, file_prefixes = default_iss_file_prefixes(), join_with_af = TRUE, pool_col = "concatenatePoolIDSeqRun", report_path = default_report_path() )
association_file |
The file system aligned association file (contains columns with absolute paths to the 'iss' folder) |
file_prefixes |
A character vector with known file prefixes to match on file names. NOTE: the elements represent regular expressions. For defaults see default_iss_file_prefixes. |
join_with_af |
Logical, if TRUE the imported stats files will be merged with the association file, if false a single data frame holding only the stats will be returned. |
pool_col |
A single string. What is the name of the pool column
used in the Vispa2 run? This will be used as a key to perform a join
operation with the stats files |
report_path |
The path where the report file should be saved.
Can be a folder, a file or NULL if no report should be produced.
Defaults to |
A data frame
Other Import functions:
import_association_file()
,
import_parallel_Vispa2Matrices()
,
import_single_Vispa2Matrix()
fs_path <- system.file("extdata", "fs.zip", package = "ISAnalytics") fs <- unzip_file_system(fs_path, "fs") af_path <- system.file("extdata", "asso.file.tsv.gz", package = "ISAnalytics" ) af <- import_association_file(af_path, root = fs, import_iss = FALSE, report_path = NULL ) stats_files <- import_Vispa2_stats(af, join_with_af = FALSE, report_path = NULL ) head(stats_files)