Package index • GetFeatistics

All functions

GetCombined_featTable_MSDial(): Combining three tables of feature intensities in a combined table.

QCs_process(): Filter a dataset of features considering pooled quality control samples.

Volcano_lm(): Generate a Volcano plot from the table of linear regression models

Volcano_ttest_FC(): Generate a Volcano plot.

addINFO_to_table(): Add the information from featINFO to a table.

add_ChemData_to_featINFO(): Add chemical data to a featINFO table.

all_PubChem_properties(): All PubChem properties

auto_scale(): Auto-scale values

build_long_vector_of_colors(): Build a vector with colors.

check_if_fix_names_needed(): Check if names can be fixed

checkmolecules_in_feat_table(): Check molecules in the feature table.

clean_transf_colnames(): Clean colnames after transformation

create_df_examples(): Create example datasets

cutP(): Cutting the P-value if < 0.001

do_FELLA_enrichment_analysis(): Perform FELLA Enrichment Analysis.

export_figures(): Export plots

export_the_table(): Export the table

fix_duplicated(): Fix duplicate names

fix_names(): Fix names

from_AnnoLevel_to_ordered_number(): Get an numeric vector from a factor vector of annotation levels.

from_ordered_number_to_AnnoLevel(): Get a factor vector of annotation levels from a numeric vector.

gentab_FC(): Generate a Table with Fold Change

gentab_FC_more_than2levels(): Generate a Table with Fold Change even if the factor has more than 2 levels

gentab_P.1wayANOVA_posthocTukeyHSD(): Generate a Table with P-values from one-way ANOVA with TukeyHSD posthoc

gentab_P.2wayANOVA_posthocTukeyHSD(): Generate a Table with P-values from two-way ANOVA with TukeyHSD posthoc

gentab_P.t.test(): Generate a Table with P-values from a T-test

gentab_descr(): Generate a table with descriptive statistics

gentab_lm_long(): Generate a long table with complete results of linear regression models

getBoxplots(): Create some simple boxplots.

getChemData(): Get Chemical data from PubChem.

getHeatMap(): Get an Heat Map.

getPCA(): Get Principal components analysis.

get_AnnoLevels_MSDial(): Get the annotation levels.

get_feat_info_from_MSDial(): Get a featINFO table from the MSDIAL export file.

get_feat_info_from_patRoon(): Get a featINFO table from the patRoon outputs.

get_feat_table_from_MSDial(): Get a table of feature intensities from the MSDIAL export file.

get_feat_table_from_patRoon(): Get a table of feature intensities from the patRoon output.

get_phase_amount(): Get the amount of mobile phases needed for a sequence.

get_targeted_elaboration(): Elaborating results of targeted analyses

mean_scale(): Mean-scale values

merge_results(): Combining results from different chromatographic/polarity sequences.

pareto_scale(): Pareto-scale values

plot_calibration_curves(): Plotting calibration curves of a targeted elaboration

range_scale(): Range-scale values

round_the_result(): Round a number to defined digital places

test_normality_Shapiro_table(): Test normality with a Shapiro–Wilk test

test_normality_density_plot(): Test normality by generating a density plot

test_normality_q_q_plot(): Test normality by generating a Q-Q plot

transf_data(): Transform the data

transpose_feat_table(): Transpose features table.

zero_prefixing(): Zero prefixing numbers