# Workflow for non-targeted LC-MS metabolic profiling

## Documentation for package ‘notame’ version 1.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

notame-package | 'notame' package.
assess_quality | Assess quality information of features
citations | Show citations
cluster_features | Cluster correlated features originating from the same metabolite
combined_data | Retrieve both sample information and features
compress_clusters | Compress clusters of features to a single feature
correct_drift | Correct drift using cubic spline
drop_flagged | Drop flagged features
drop_qcs | Drop QC samples
finish_log | Finish a log
fix_MSMS | Transform the MS/MS output to publication ready
fix_object | Fix object for functioning of notame
flag | Get and set the values in the flag column
flag<- | Get and set the values in the flag column
flag_contaminants | Flag contaminants based on blanks
flag_detection | Flag features with low detection rate
flag_quality | Flag low-quality features
flag_report | A report of flagged features
hilic_neg_sample | Toy data set
hilic_pos_sample | Toy data set
import_from_excel | Read formatted Excel files
import_from_msdial | Import data from a TSV file created by MS-DIAL
impute_rf | Impute missing values using random forest
impute_simple | Simple imputation
init_log | Initialize log to a file
inverse_normalize | Inverse-rank normalization
join_colData | Join new columns to pheno data
join_rowData | Join new columns to feature data
log_text | Log text to the current log file
mark_nas | Mark specified values as missing
merge_notame_sets | Merge SummarizedExperiment objects together
notame | 'notame' package.
pca_bhattacharyya_dist | Bhattacharyya distance between batches in PCA space
perform_repeatability | Compute repeatability measures
pqn_normalization | Probabilistic quotient normalization
quality | Extract quality information of features
rp_neg_sample | Toy data set
rp_pos_sample | Toy data set
ruvs_qc | Remove Unwanted Variation (RUV) between batches
toy_notame_set | Toy data set
write_to_excel | Write results to Excel file