The MFAssignR package was designed for multi-element molecular formula (MF) assignment of ultrahigh resolution mass spectrometry measurements. A number of tools for internal mass recalibration, MF assignment, signal-to-noise evaluation, and unambiguous formula selections are provided.
This PR deals with fixing the Recal function bugs and covers multiple issues.
three new arguments were added to the processKnown function: type (A molecule type of the annotation), multiplier (The multiplier for the num column) and element_mass (The mass of the group used for correction), as well as the original type argument was renamed to type_col (The column name to store the type of compound).
the type_col column is now computed using the multiplier (1 for O, 2 for H): step_result[[type_col]] <- step_result[[type_col]] + step_result[[num_col]]*multiplier
paste function to create the form column was not working, so it was corrected as follows:
step_result <- dplyr::mutate(
step_result,
form=paste(C, H, O, N, S, P, E, S34, N15, D, Cl, Fl, Cl37, M, NH4, POE, NOE, sep="_")
)
columns were incorrectly deleted in here: step_result <- step_result[-remove_indices] . Now only `[-remove_indices] is used instead of original [-remove_indices, ]
processKnown function is now used also if cols == 3, not only cols == 2
Accompanying test and test data to replicate the bug are also included.
This PR deals with fixing the Recal function bugs and covers multiple issues.
processKnownfunction:type(A molecule type of the annotation),multiplier(The multiplier for the num column) andelement_mass(The mass of the group used for correction), as well as the originaltypeargument was renamed totype_col(The column name to store the type of compound).type_colcolumn is now computed using the multiplier (1 for O, 2 for H):step_result[[type_col]] <- step_result[[type_col]] + step_result[[num_col]]*multiplierformcolumn was not working, so it was corrected as follows:step_result <- step_result[-remove_indices]. Now only `[-remove_indices] is used instead of original [-remove_indices, ]processKnownfunction is now used also ifcols == 3, not onlycols == 2Accompanying test and test data to replicate the bug are also included.
Related issues: