Man pages for metamorphr
Tidy and Streamlined Metabolomics Data Workflows
| atoms | A tibble containing the NIST standard atomic weights |
| calc_km | Calculate the Kendrick mass |
| calc_kmd | Calculate the Kendrick mass defect (KMD) |
| calc_neutral_loss | Calculate neutral losses from precursor ion mass and fragment... |
| calc_nominal_km | Calculate the nominal Kendrick mass |
| collapse_max | Collapse intensities of technical replicates by calculating... |
| collapse_mean | Collapse intensities of technical replicates by calculating... |
| collapse_median | Collapse intensities of technical replicates by calculating... |
| collapse_min | Collapse intensities of technical replicates by calculating... |
| convert_from_matrix | Convert a wide matrix to a tidy tibble |
| convert_from_wide | Convert a wide feature table to a tidy tibble |
| create_metadata_skeleton | Create a blank metadata skeleton |
| filter_blank | Filter Features based on their occurrence in blank samples |
| filter_cv | Filter Features based on their coefficient of variation |
| filter_global_mv | Filter Features based on the absolute number or fraction of... |
| filter_grouped_mv | Group-based feature filtering |
| filter_msn | Filter Features based on occurrence of fragment ions |
| filter_mz | Filter Features based on their mass-to-charge ratios |
| filter_neutral_loss | Filter Features based on occurrence of neutral losses |
| formula_to_mass | Calculate the monoisotopic mass from a given formula |
| impute_bpca | Impute missing values using Bayesian PCA |
| impute_global_lowest | Impute missing values by replacing them with the lowest... |
| impute_knn | Impute missing values using nearest neighbor averaging |
| impute_lls | Impute missing values using Local Least Squares (LLS) |
| impute_lod | Impute missing values by replacing them with the Feature... |
| impute_mean | Impute missing values by replacing them with the Feature mean |
| impute_median | Impute missing values by replacing them with the Feature... |
| impute_min | Impute missing values by replacing them with the Feature... |
| impute_nipals | Impute missing values using NIPALS PCA |
| impute_ppca | Impute missing values using Probabilistic PCA |
| impute_rf | Impute missing values using random forest |
| impute_svd | Impute missing values using Singular Value Decomposition... |
| impute_user_value | Impute missing values by replacing them with a user-provided... |
| join_metadata | Join a featuretable and sample metadata |
| metamorphr-package | metamorphr: Tidy and Streamlined Metabolomics Data Workflows |
| msn_calc_nl | Calculate neutral losses from precursor ion mass and fragment... |
| msn_scale | Scale intensities in MSn spectra to the highest value within... |
| normalize_cyclic_loess | Normalize intensities across samples using cyclic LOESS... |
| normalize_factor | Normalize intensities across samples using a normalization... |
| normalize_median | Normalize intensities across samples by dividing by the... |
| normalize_pqn | Normalize intensities across samples using a Probabilistic... |
| normalize_quantile_all | Normalize intensities across samples using standard Quantile... |
| normalize_quantile_batch | Normalize intensities across samples using grouped Quantile... |
| normalize_quantile_group | Normalize intensities across samples using grouped Quantile... |
| normalize_quantile_smooth | Normalize intensities across samples using smooth Quantile... |
| normalize_ref | Normalize intensities across samples using a reference... |
| normalize_sum | Normalize intensities across samples by dividing by the... |
| pipe | Pipe operator |
| plot_pca | Draws a scores or loadings plot or performs calculations... |
| plot_volcano | Draws a Volcano Plot or performs calculations necessary to... |
| read_featuretable | Read a feature table into a tidy tibble |
| read_featuretable_mzmine | Read a 'full_feature_table' from 'mzmine' into a tidy tibble |
| read_mgf | Read a MGF file into a tidy tibble |
| remove_empty_cols | Remove empty columns from a tibble or data frame |
| scale_auto | Scale intensities of features using autoscale |
| scale_center | Center intensities of features around zero |
| scale_level | Scale intensities of features using level scaling |
| scale_pareto | Scale intensities of features using Pareto scaling |
| scale_range | Scale intensities of features using range scaling |
| scale_vast | Scale intensities of features using vast scaling |
| scale_vast_grouped | Scale intensities of features using grouped vast scaling |
| summary_featuretable | General information about a feature table and sample-wise... |
| toy_metaboscape | A small toy data set created from a feature table in... |
| toy_metaboscape_metadata | Sample metadata for the fictional dataset 'toy_metaboscape' |
| toy_mgf | A small toy data set containing MSn spectra |
| transform_log | Transforms the intensities by calculating their log |
| transform_power | Transforms the intensities by calculating their _n_th root |
