View source: R/construct_database.R
construct_database | R Documentation |
Construct MS2 spectra database according to mzXML data and compound information table (csv format).
construct_database(
path = ".",
version = "0.0.1",
metabolite.info.name = "metabolite.info.csv",
source = "Michael Snyder Lab",
link = "http://snyderlab.stanford.edu/",
creater = "Xiaotao Shen",
email = "shenxt1990@163.com",
rt = TRUE,
mz.tol = 15,
rt.tol = 30,
threads = 3
)
path |
Work directory. |
version |
The version of you database. Default is 0.0.1. |
metabolite.info.name |
The metabolite information table name, it must be csv format. The demo data can be got from the 'demoData' package. Please see https://tidymass.github.io/metid/articles/metid.html |
source |
The source of your database. |
link |
Website link of the source. |
creater |
Creater name. For example, Xiaotao Shen. |
email |
email address. |
rt |
Do the metabolites have RT information or not?. If not, set it as FALSE. |
mz.tol |
m/z tolerance for the match between metabolites and precursor m/z of MS2 spectra. |
rt.tol |
RT tolerance for the match between metabolites and precursor m/z of MS2 spectra. |
threads |
The number of threads |
A databaseClass object.
Xiaotao Shen shenxt1990@outlook.com
The example and demo data of this function can be found https://tidymass.github.io/metid/articles/metid.html
## Not run:
database0.0.1 <- construct_database(
path = ".",
version = "0.0.1",
metabolite.info.name = "metabolite.info.csv",
creater = "dumine",
email = "dumine@zju.edu.cn",
rt = FALSE,
mz.tol = 15,
rt.tol = 30,
threads = 5
)
## End(Not run)
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