Get a featINFO table from the patRoon outputs.
get_feat_info_from_patRoon.RdGiven the featureGroups, components, and MFsummary tables, it creates the featINFO table, i.e. the table with the full information for each feature.
Usage
get_feat_info_from_patRoon(
patRoon_featureGroups,
patRoon_MFsummary = NULL,
MFsummary_score_columns = c("individualMoNAScore", "score"),
add_AnnoLevels = FALSE
)Arguments
- patRoon_featureGroups
dataframe. Features groups and related intensities obtained after XCMS. This table should contain the feature group names in a column named "group", the retention times a column named "ret", the m/z ratio in a column named "mz", and the intensities in all other columns.
- patRoon_MFsummary
NULL or a dataframe obtained from converting as.data.table the output of the function generateCompounds from patRoon. At least the column named "group" and "score" must be present, and if multiple molecules are annotated for each feature group, the one with the top score as provided in the MFsummary_score_columns argument will be considered.
- MFsummary_score_columns
character of length 1 or more. The name of the column(s) of patRoon_MFsummary that will be used as prioritization score to assign the candidate. The first provided column will be used at first, if that score is tied, the second provided column will be considered, and so for.
- add_AnnoLevels
logical. If TRUE, and if a MFsummary table was loaded with suitable individualMoNAScore, an additional column named "AnnoLevels" will be added, and the annotation levels will be calculated considering the cut-offs reported in https://doi.org/10.1007/s00216-022-04207-z.