Check molecules in the feature table.
checkmolecules_in_feat_table.RdGiven a featINFO, a feature intensities table, and a table with a list of molecules with known mass, it looks for those molecule in the feature table.
Usage
checkmolecules_in_feat_table(
featmatrix,
featinfo,
molecules_list,
mz_to_search = NULL,
error = 20,
error_type = "ppm",
check_rt = FALSE,
rt_to_search = NULL,
rt_window = 12
)Arguments
- featmatrix
a dataframe: first column the featname, each other column is a sample with feature intensities. Each row is a feature. It can be obtained with the get_feat_table_from_MSDial function of the present package.
- featinfo
a dataframe. A table with at least three columns, in this order: feature names, retention times, and masss-to-charge ratios. It can be obtained with the get_feat_info_from_MSDial function of the present package.
- molecules_list
a dataframe containing the molecules to search. The first column must contain the names of the molecule. ALso it should contain at least another column with the m/z to look for.
- mz_to_search
character vector of length 1. It is the column name of the molecules_list data-frame with the m/z values to look for (it not provided the third column will be used).
- error
numeric of length 1. Is is the tolerance for the search of m/z in Da or ppm (specified in the error_type argument)
- error_type
one of the following: "ppm", or "Da". It is referred to the value provided in the error argument.
- check_rt
logical. Should also the retention times be checked?
- rt_to_search
if check_rt is TRUE, it is the column name of the molecules_list data-frame with the rt values to look for. (it not provided the second column will be used)
- rt_window
numeric of length 1. It is the retention time window to consider centered to the known molecules to check the experimental ones. Please check that the unit (seconds or minutes) is the same in all tha tables.