Man pages for nicohuttmann/htmnanalysis
Analysis of Omics Data
| addPrepro | Additional preprocessing of raw data |
| adjacency | Similaryty to adjacency |
| benjaminiHochbergCorrection | Does Benjamini-Hochberg correction |
| build.GOannotaions | Builds GO annotation database |
| cgroups | Combines groups |
| cleanUp | Cleanup function |
| cm0 | Removes columns/proteins based on fraction of entries equal 0 |
| cmna | Removes columns and rows from correlation matrix with many... |
| cmsd | Removes columns/proteins based on standard deviation |
| cmv02 | Returns column names/proteins that have more entries above 0... |
| combineAND | Combines logical vectors using and |
| combine.groups | Sums up numerical and logical data groupwise |
| combineOR | Combines logical vectors using or |
| connectivityFromCor | Returns protein connectivity values from correlation data |
| connectivityFromCor.rel | Returns normalized protein connectivity values from... |
| connectivityFromExpr | Returns protein connectivity from expression data |
| connectivityFromExpr.rel | Returns normalized protein connectivity values from... |
| contain.list | Serches list entries for given element and returns T/F vektor... |
| corMatrix | Computes and plots correlation matrix |
| cor.object | Creates list containing correlation matrix relevant objects |
| create_protein.db | Combines protein information from raw data frames |
| createTraitTable | Writes template for traits |
| ct | Cuts dendrogram and returns names of proteins from specified... |
| cv | Returns coefficients of variations for columns/ proteins |
| d | Prints all data names |
| dataProcessing | Data processing |
| define.groups | Extracts row names from data frame and let's user define... |
| enrichGO | GO term enrichment using Fisher's exact test |
| enrichGOGroups | GO term enrichment using Fisher's exact test |
| extractData | Extracts data frames from raw data |
| extractRownames | Extracts row names and filters based on columns |
| extractRownames1 | Extracts row names and filters based on one column |
| extractRownames2 | Extracts row names and filters based on 2 columns |
| factorizeMatrix | Divides each row of a matrix by the elements of the specified... |
| fisherTestGO | Performs Fisher's exact test for enrichment of GO annotation... |
| gapply | Applies given function to given groups separately |
| geomean | Computes the geometric mean |
| getALLProteins | Returns vector of proteins annotated to given GO term |
| getData | Find data |
| getDataFrame | Finds and returns data frame |
| getList | Defines basic data list |
| getMedianNormalizationFactors | Returns factors from PQN normalization |
| getNames | Finds and returns the column or row names of a data frame |
| getNumber | Let's user define a number |
| getSampleGroup | Finds group vector |
| getVector | Builds vector |
| getVector1 | Finds and returns one vector |
| importRawData | Imports raw data frame |
| importTraitData | Imports trait table |
| impute_normd | Imputes missing values from normal distribution |
| loadRawData | Loads raw.data from saved rawdata.RData file |
| make.ranges | Return ranges with given width from numbers |
| meanAbsCor | Returns mean absolute correlation coefficient |
| meanCor | Returns mean correlation coefficient from correlation matrix |
| medianAbd | Returns median abundance of proteins/columns |
| medianFactor | Returns row median of factorized matrix |
| modifyNames | Modify column names of data frame |
| n | Returns normalized data from PQN normalization see... |
| new.cache | Generate new cache list |
| new_dat | Generate new data data frame |
| new_raw_data | Generate new raw data data frame |
| nf | Returns factors from PQN normalization see... |
| ok | Ok function to ask for yes or no |
| plot_corMatrix | Plots correlation matrix |
| plot_dendrogram | Plots dendrogram |
| plot_marker | Prints marker bar and lines of proteins for correlation... |
| plot_varianceDendrogram | Plots variances of clusters |
| plot_venn2 | Plots venn diagram from three samples |
| plot_venn3 | Plots venn diagram from three samples |
| printn | Prints names with numbers |
| processQualitativeData | Substitutes qualitative data |
| removePrefix | Removes vector entries based on specified prefix |
| save.ggplot | Saves ggplots |
| saveThatShit | Saves main data frames |
| saveThis | Saves data in basic data structure |
| s.cache | Saves cache list in dat or other list |
| setColRowNames | Changes colnames to universal namees and rownames to proteins... |
| setSampleGroups | Names a group vector with groups to use |
| similarity | Similarity from correlation |
| simplePCA | Simple PCA plot |
| start0 | Start function to build list structures |
| storeRawData | Stores and deletes raw.data |
| studentstTest | Performs student's t-test and stores data |
| subsetVector | Set a sub group |
| transposeData | Transpose data frames |
| tri | Reduces data frame to vector of lower triangle |
| ttestdown | Returns downregulated proteins from ttest dataframe |
| ttestup | Returns upregulated proteins from ttest dataframe |
| wd | Sets given working directory |
| whatToDo | Enables to choose between options |
