read_mzml {chromConverter} | R Documentation |
Read mzML files
Description
Extracts data from mzML
files using parsers from either RaMS or mzR.
The RaMS parser (default) will only return data in tidy (long) format. The
mzR parser will return data in wide format. Currently the mzR-based parser
is configured to return only DAD data.
Usage
read_mzml(
path,
format_out = c("matrix", "data.frame", "data.table"),
data_format = c("long", "wide"),
parser = c("RaMS", "mzR"),
what = c("MS1", "MS2", "BPC", "TIC", "DAD", "chroms", "metadata", "everything"),
verbose = FALSE,
...
)
Arguments
path |
Path to |
format_out |
Class of output. Only applies if |
data_format |
Whether to return data in |
parser |
What parser to use. Either |
what |
What types of data to return (argument to |
verbose |
Argument to |
... |
Additional arguments to |
Value
If RaMS
is selected, the function will return a list of "tidy"
data.table
objects. If mzR
is selected, the function will return a
chromatogram in matrix
or data.frame
format according to the
value of format_out
.
Author(s)
Ethan Bass