Workflow for non-targeted LC-MS metabolic profiling

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Documentation for package ‘notame’ version 1.0.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
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