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Check molecules in the feature table.

checkmolecules_in_feat_table.Rd

Given 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,
  return_as_featinfo_lev1 = FALSE
)

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 or get_feat_table_from_patRoon function).

featinfo

a dataframe. A table with at least three columns, in this order: feature names, retention times, and mass-to-charge ratios. (It can be obtained with the get_feat_info_from_MSDial or get_feat_info_from_patRoon function).

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.

character vector of length 1. It is the column name of the molecules_list data-frame with the m/z values to look for (If 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?

if check_rt is TRUE, it is the column name of the molecules_list data-frame with the rt values to look for. (If 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 the tables.

return_as_featinfo_lev1

logical. If TRUE, and if also check_rt is TRUE, the function will return the featinfo with the found molecules as level 1 in the AnnoLevel column.

Value

A tibble with the matching feature intensities. If return_as_featinfo_lev1 is TRUE, the output is instead the featinfo with the compounds found as level 1 in the AnnoLevel column.