all_subset | Identifies the 'subset' of All Features |
analysis_log | Creates R markdown document report |
anova_filter | Identifies biomolecules to be filtered in preparation for... |
anova_test | Tests for a quantiative difference between groups (aka... |
applyFilt | Apply a S3 filter object to a pmartR S3 object |
as.isobaricpepData | Convert Data to Appropriate pmartR Class |
as.lipidData | Convert Data to Appropriate pmartR Class |
as.metabData | Convert Data to Appropriate pmartR Class |
as.multiData | Create a 'multiData' object from multiple omicsData objects |
as.nmrData | Convert Data to Appropriate pmartR Class |
as.pepData | Convert Data to Appropriate pmartR Class |
as.proData | Convert Data to Appropriate pmartR Class |
bpquant | Runs BP-Quant |
bpquant_mod | bpquant_mod function |
combine_lipidData | Combines two omicsData objects with identical sample... |
combine_techreps | Combine technical replicates of an omicsData object |
complete_mols | Identify biomolecules with no missing values across samples |
cor_result | Correlation matrix of biomolecule data |
create_comparisonDF | Returns data.frame with comparisons to be made |
custom_filter | Custom Filter |
custom_sampnames | Creates custom sample names for plots |
cv_filter | Filter Based on Pooled Coefficient of Variation (CV) Values |
dim_reduction | Reduce Dimension of Data for Exploratory Data Analysis |
edata_replace | Replace Values Equal to x with y |
edata_summary | Creates a list of six Data Frames, one for each summarizing... |
edata_transform | Apply a Transformation to the Data |
find_fmeta_cnames | Find column names in f_meta for each object. May return in... |
fit_surv | Basic survival analysis function |
fmeta_matches | Check that the f_meta file contains a column aligned to each... |
get_check_names | Fetch the check.names attribute |
get_comparisons | Return comparisons of statRes object |
get_data_class | Return data_class of statRes or trellData object |
get_data_info | Fetch the data_info attribute |
get_data_norm | Fetch the normalization status of the data |
get_data_scale | Fetch the current data scale |
get_data_scale_orig | Fetch the original data scale |
get_edata_cname | Fetch the e_data column name |
get_emeta_cname | Fetch the e_meta column name |
get_fdata_cname | Fetch the f_data column name |
get_filters | Fetch the filters attribute |
get_group_DF | Fetch the group_DF attribute |
get_group_table | Get group table |
get_isobaric_info | Fetch the isobaric_info attribute |
get_isobaric_norm | Fetch the isobaric normalization info |
get_meta_info | Fetch the meta_info attribute |
get_nmr_info | Fetch the nmr_info attribute |
get_nmr_norm | Fetch the NMR normalization info |
get_spans_params | Gets the parameters for the highest ranked methods from... |
group_comparison_anova | Group comparisons for the anova test |
group_comparison_imd | Group comparisons for the g-test |
group_designation | Creates Attribute of omicsData object containing Group... |
gtest_filter | Identifies peptides to be filtered out in preparation for... |
gtest_heatmap | Plot a heatmap for the g-test results of imd-anova |
hello | Hello, World! |
imd_anova | Tests for a qualitative and quantitative difference between... |
imdanova_filter | IMD-ANOVA filter object |
imd_test | Tests for the independence of missing data across groups (aka... |
los | Identify Features from the Top L Order Statistics |
mad_transform | Median Absolute Deviation Transformation |
make_volcano_plot_df | Create a plotting dataframe for volcano plots and heatmaps. |
mean_center | Mean Center Transformation |
median_center | Median Center Transformation |
missingval_result | Creates an object of class naRes |
molecule_filter | Molecule filter object |
MSnSet2pepData | Convert Data of class MSnSet to pmartR pepData Class |
nonmissing_per_group | Computes the Number of Non-Missing Data Points by Group |
normalize_global | Calculate Normalization Parameters |
normalize_global_basic | Normalize e_data within SPANS |
normalize_isobaric | Normalize an object of class isobaricpepData |
normalize_loess | Loess Normalization |
normalize_nmr | Normalize an object of class nmrData |
normalize_quantile | Quantile Normalization |
normRes_tests | Test the location and scale parameters from a normalization... |
p_adjustment_anova | Adjust p-values for multiple comparisons |
plot-corRes | plot.corRes |
plot-customFilt | plot.customFilt |
plot-cvFilt | plot.cvFilt |
plot-dataRes | Plots an object of class dataRes |
plot-dimRes | plot.dimRes |
plot-imdanovaFilt | plot.imdanovaFilt |
plot-isobaricnormRes | Plots an object of class isobaricnormRes |
plot-isobaricpepData | plot.isobaricpepData |
plot_km | Basic survival analysis plot |
plot-lipidData | plot.lipidData |
plot-metabData | plot.metabData |
plot-moleculeFilt | plot.moleculeFilt |
plot-naRes | Plots an object of class naRes |
plot-nmrData | plot.nmrData |
plot-nmrnormRes | Plots an object of class nmrnormRes |
plot-normRes | plot.normRes |
plot-pepData | plot.pepData |
plot-proData | plot.proData |
plot-proteomicsFilt | plot.proteomicsFilt |
plot-rmdFilt | plot.rmdFilt |
plot-SPANSRes | Plots an object of class SPANSRes |
plot.statRes | Plotting function for 'statRes' objects |
pmartR | My package |
pmartR_filter_worker | Remove items that need to be filtered out |
ppp | Identify Proportion of the Peptides Present (PPP)... |
ppp_rip | Identify Proportion of Peptides Present (PPP) and Rank... |
pquant | Protein Quantitation using Mean or Median Peptide Abundances |
pre_imdanova_melt | Create a Melted and Grouped Version of e_data for IMD_ANOVA... |
prep_flags | Extract flag columns from a statRes object |
print-customFilt | print.customFilt |
print-cvFilt | print.cvFilt |
print.cvFilterSummary | Print method for summary of CV filter |
print-dataRes | print.dataRes |
print-imdanovaFilt | print.imdanovaFilt |
print.imdanovaFilterSummary | Print method for summary of imdanova filter |
print-lipidData | print.lipidData |
print-metabData | print.metabData |
print-moleculeFilt | print.moleculeFilt |
print.moleculeFilterSummary | Print method for summary of molecule filter |
print-normRes | print.normRes |
print-pepData | print.pepData |
print-proData | print.proData |
print-proteomicsFilt | print.proteomicsFilt |
print.proteomicsFilterSummary | Print method for summary of proteomics filter |
print-rmdFilt | print.rmdFilt |
protein_quant | protein_quant wrapper function |
proteomics_filter | Proteomics filter object |
qrollup | Applies qrollup function |
reexports | Objects exported from other packages |
replace_zeros | Replace 0 with NA |
report_dataRes | Creates a data frame displaying multiple metrics |
rip | Identify Rank-Invariant Peptides |
rmd_conversion | Conversion between log2(RMD) and p-value |
rmd_filter | RMD Runs |
rrollup | Applies rrollup function |
run_group_meancor | Calculate the Mean Correlation of a Sample with Respect to... |
run_kurtosis | Calculate the Kurtosis of Sample Runs |
run_mad | Calculate the Median Absolute Deviance (MAD) of Sample Runs |
run_prop_missing | Calculate the Fraction of Missing Data of Sample Runs |
run_skewness | Calculate the Skewness of Sample Runs |
set_check_names | Set check.names attribute of omicsData object |
spans_make_distribution | Creates the list of median p-values used to make the... |
spans_procedure | Calculate SPANS Score for a Number of Normalization Methods |
statres_barplot | Fold change barplots for statres objects |
statRes-class | statRes class. |
statRes_output | Function to take raw output of 'imd_anova' and create output... |
statres_volcano_plot | Volcano plot for the anova results of imd-anova |
summary.customFilt | Produce a basic summary of a custom_filter object |
summary.cvFilt | Produce a basic summary of a cv_filter object |
summary.imdanovaFilt | Produce a basic summary of a imdanova_filter object |
summary-isobaricnormRes | Summarizes an object of class isobaricnormRes |
summary_km | Basic survival analysis summary |
summary.moleculeFilt | Produce a basic summary of a molecule_filter object |
summary-nmrnormRes | Summarizes an object of class nmrnormRes |
summary-omicsData | Produce a basic summary of a pmartR omicsData S3 Object |
summary-pmartR-results | Produce summaries of various results objects from pmartR... |
summary.proteomicsFilt | Produce a basic summary of a proteomics_filter object |
summary.rmdFilt | Produce a basic summary of a rmd_filter object |
surv_designation | Create a "surv_DF" attribute so that survival analysis can be... |
take_diff | Compute pairwise differences |
vector_replace | Replace x with y for a single vector |
write_stat_results | Creates a list of three sheets, Normalized Data, DA Test... |
write_stat_results_omics | Creates a list of three sheets, Normalized Data, DA Test... |
zrollup | Applies zrollup function |
zscore_transform | Z-Score Transformation |
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