| aheatmap | A function to draw clustered heatmaps. |
| aheatmap2 | a wrapper to aheatmap which enables passing phenoData. This... |
| aheatmat | annotated heatmap using heatmat engine |
| aheatmatcor | plot correlation heatmap for rows from a matrix |
| aMatrix | plot matrix values |
| anovaP | ANOVA test P value |
| aoMatrix | plot an ordered (sorted) matrix |
| augmentMatrixColumnByID | Augment a matrix by ID in the direction of columns |
| augmentMatrixColumnByID_update | update augMat after it is subsetted |
| augmentMatrixRowByID | Augment a data frame by ID in the direction of rows |
| autocolpal4DF | get default colorpal (color vector) for a data frame... |
| BootstrapGenes | Consensus clustering based on BootstrapClusterTest from OOMPA |
| buildapp | build an openCPU app with... |
| buildapp0 | build an openCPU app with build+install+opencpu$browse |
| buildSilhouette | extract silhouette information for clustering |
| categorizePvec | convert P value into categories |
| cluster_mat | hierarchical clustering with rows using given distance and... |
| colorpalette2colvec | extracts color given a specified pallete (string) possibly... |
| combine_cormat | when pearson and spearman values both are desired, we can fit... |
| convert_annotations | convert annotation (data frame) and annotation_colors (a... |
| cophCorFromConsMat | calculate cophenetic coefficient for a consensus matrix... |
| copheneticCoef | calculate cophenetic coefficient for a hierarchical... |
| corTest | correlation betweent two vector |
| coxphP2 | cox PH P value |
| create_bum | Create a bum 'object' |
| decideOrder | 2-step procedure to decide ordering |
| df_force_factor | force selected columns of a data frame as factor |
| df_format_df | format a data frame by imposing non-continuous variables as... |
| dichotomizeExpr | dichotomize expression into binary based on BI or quantile |
| dichotomizeExpr_BI | dichotomize expression into binary based on BI |
| dichotomizeExpr_quantile | dichotomize expression into Low/High group |
| dispersionFromConsMat | calculate dispersion from a consensus matrix extracted from... |
| doccoRmd | generate html from Rmd with docco-linear style as in <URL:... |
| emptydfFromDF | there may be mroe elegant ways to do this |
| fitSIBERonMat | fit SIBER on a matrix, one row at a time |
| fitSIBERonMat_Bygroup | fit SIBER on matrix but split by group |
| fn_TWanova | two way anova test for a given response and two vectors |
| formatAnnotation4aheatmap | Prepare annotation data frame so that aheatmap can show it |
| formatDF | format a data frame using formatVec |
| formatLevel | formatting a given vector according to given levels |
| formatVec | format a vector by forcing into a factor if not numeric or... |
| genbreaks | generate breaks for specified start, end position and n,... |
| generate_breaks | generate breaks for an input matrix or vector |
| generate_breaks0 | when center=TRUE, the broken bars at 0 has equal length of... |
| getDefaultBarColList | sometimes we just want a default barColList rather than... |
| getfisherP | compute fisher exact test (chisq test when failure) p value... |
| get_pal | obtain color pallete defined in this package |
| getPvecSmry | given a p value vector and a vector of cutoffs, find number... |
| get_stretch | compute stretch from a continuous map |
| getter | general getter function for attributes in an object |
| getter.augMat | get method for class augMat |
| getter.colpal4DF | get method for class colpal4DF |
| getter.rowanovaMatVec | get method for class rowanovaMatVec |
| getter.rowcorMatVec | get method for class rowcorMatVec |
| getter.rowttestMatVec | get method for class rowttestMatVec |
| getTopNindex | get top N elements from a vector and return a vector of index... |
| getTopNvalue | get top N elements from a vector |
| ggKM | plot OS against a continuous variable by breaking the... |
| ggKMcat | for categorical covariate x, plot KM curve |
| guessAlpha | guess alpha |
| guessAlpha_line | guess alpha in a line plot |
| guess_angle | guess angle for axis angle |
| guessCEX | given number of genes G in a heatmap, guess rowCEX to be... |
| guess_nrowL | guess nrowL from a specified number of categories |
| heatm | Generic heatm method |
| heatm.rowcorMatVec | Heatmap plot for rowcorMatVec class |
| heatm.rowttestMatVec | Heatmap plot for rowttestMatVec class |
| hist.rowanovaMatVec | Bum plot for rowanovaMatVec class |
| hist.rowcorMatVec | Bum plot for rowcorMatVec class |
| hist.rowfisherMatVec | Bum plot for rowfisherMatVec class |
| hist.rowpairedttestMatVec | Bum plot for rowpairedttestMatVec class |
| hist.rowttestMatVec | Bum plot for rowttestMatVec class |
| hist.rowTWanovaMatVec | Bum plot for rowTWanovaMatVec class |
| isCat | check if a vector is categorical or continuous |
| iscatDF | check columnwise of a data frame whether it is categorical... |
| isCont | index of columns of a data frame is continuous (numeric) |
| is_continuous | guess if a vector is continuous |
| isTopN | return a logical vector if elements in a vector is top N... |
| ixglobal2local | map global index to local index given reference |
| ixlocal2global | map local index to global index given reference |
| ixunify2index | unify index/name indexing into global index given global name |
| lm_xy | lm for cont x and y |
| logic2sortedIndex | conver logic vector to sorted index vector |
| makeColMat | prepare a matrix for plotting by converting it to a color... |
| makestring | impose as.character |
| mapNames | mapping a vec to another name space |
| mapNames4mat | for a matrix, i.e. 0, 1, we may want to format it as WT, MUT |
| maskByLimit | mask values as NA in a matrix |
| mylibrary | multiple scatter plot for a given data frame |
| namedColVec | Generate a named color vector |
| name-of-the-vec-as-in-the-named-list-of-colpal | build a map given a vector of values and color pallete |
| noNA | remove NA cases for either a vector, matrix or data frame |
| nonNumeric2FactorByColumn | force to factor when non-numeric |
| n_unique | return the number of unique values |
| overwritef | a wrapper for file overwrite |
| pairedttestP | paired t-test |
| parse_coxphP2 | parse the coxphP2() returned value to text so as to show OR,... |
| pdfOR | pdf() with overwrite option |
| plainRmd | generate html with plain style |
| plot4rowanovaMatVec | ordered horizontal bar plot for rowanovaMatVec |
| plot4rowcorMatVec | ordered bar plot for rowcorMatVec class |
| plot4rowttestMatVec | ordered horizontal bar plot for rowttestMatVec |
| plotBumFDR | plot bum with FDR table on it |
| plotCatCat | plot cat-cat |
| plotCCC | Calculates Concordance Correlation Coefficient (CCC) to... |
| plot.colpal4DF | plot method for colpal4DF |
| plotContCat | plot Cont-Cat variable |
| plotContCont | plot Cont-Cont variable |
| plot.fn_TWanova | Plot method for fits from two-way data by fn_TWanova |
| plotHeatmap | present a heatmap |
| plotHeatmapTable | plot a table with colour indicated |
| plotKM | flexible KM curve wrapper |
| plotKM0 | plot just KM |
| plotMeanSD4mat | plot mean vs sd for a matrix for quick QC/filtering |
| plot.phm | plot method for phm class |
| plot.prepcolbar | plot method for prepcolbar class |
| plot.rowanovaMatVec | Bar plot for rowanovaMatVec class |
| plot.rowcorMatVec | Bar plot for rowcorMatVec class |
| plot.rowttestMatVec | Bar plot for rowttestMatVec class |
| plotScatter | flexible scatter plot (a wrapper) |
| plotSummaryFromConsensusClusterPlus | plot the fit from ConsensusClusterPlus() |
| polrP | ordinal regression for association between an ordered... |
| prepare4aheatmap | given a mat and phenoDat and barColList, calculates... |
| prepare4ColList | given a list of barColors and phenoData, prepare a list of... |
| prepcolbar | build colmat/colmap given pheno (colwise of data frame) and... |
| prepDat4pairedttest | given a vector of data (continuous) and class (binary) and... |
| print.phm | print method for phm class |
| printPvecSmry | given a p value vector and a vector of cutoffs, find number... |
| rcor | rcorr to compute correlation coefficient among columns. |
| rcorrTest | computes correlation between two vectors |
| rowanovaMatVec | ANOVA between rows of a matrix and a vector |
| rowcorMatMat_L | extension of rowcorMatVec |
| rowcorMatVec | Calculate correlation between rows of a matrix and a vector |
| rowcorMatVec_Bygroup | the grouped version for rowcorMatVec |
| rowdoMatVec_Bygroup | the driver of grouped version calculations, enpowering... |
| rowfisherMatVec | Perform Fisher Exact test between rows of mat (categorical)... |
| rowkmMatVec | Perform log rank test between rows of mat (categorical) and a... |
| rowlmMatVec | Fit a linear model with rows of mat and vec, possibly adding... |
| rowMatVecDo | perform operations between rows of a mat and a vector |
| rowpairedttestMatVec | Paired t test between rows of a matrix and a vector |
| rowranktestMatVec | compute rank test P as well as a t test result |
| rowttestMatMat_L | extension of rowttestMatVec |
| rowttestMatVec | Perform t test between rows of mat and a vector; Notice... |
| rowTWanovaMatVec | Two-way ANOVA between rows of a matrix and two vectors: two... |
| RPPAdat | An example KEGG Gene2Annotation data |
| safelog | log transformation of matrix, i.e. count matrix |
| saveOR | save() with overwrite option |
| scale_mat | scale a matrix by row, by column or none |
| scatter | Generic scatter method |
| scatter_rowanovaMatVec | scatter plot for rowanovaMatVec |
| scatter.rowanovaMatVec | Scatter plot for rowanovaMatVec class: each row produces a... |
| scatter_rowcorMatVec | scatter plot for rowcorMatVec |
| scatter.rowcorMatVec | Scatter plot for rowcorMatVec class: each row produces a... |
| scatter.rowfisherMatVec | Scatter plot for rowfisherMatVec class: each row produces a... |
| scatter.rowkmMatVec | Scatter plot for rowkmMatVec class: each row produces a... |
| scatter.rowpairedttestMatVec | Scatter plot for rowpairedttestMatVec class: each row... |
| scatter_rowttestMatVec | Scatter plot for rowttestMatVec |
| scatter.rowttestMatVec | Scatter plot for rowttestMatVec class: each row produces a... |
| scatter_rowTWanovaMatVec | scatter plot for rowanovaMatVec |
| scatter.rowTWanovaMatVec | Scatter plot for rowTWanovaMatVec class: each row produces a... |
| selectGeneFromMeanSD | select genes based on mean~SD plot from plotMeanSD4mat |
| SIBER2 | Compute BI for a gene expression matrix |
| statContCont | Calculate statistics for continuous variable x and y |
| str_extract2 | extract string given a pattern using back reference... |
| subsetMainMat | subset main expression mat |
| s_unique | unique values sorted |
| swap | swap two variables in a given environment |
| testObject | Test if an object exist |
| testree | Generic testree method (for phm object produced by... |
| testree.phm | testree method for class phm |
| test_tree_split | test association between tree cut and a vector |
| theme_base | a theme mimic the base system |
| toFC | given expression mean difference, transforms back to fold... |
| toNaturalVar | convert R variable names (i.e. from read table with default... |
| transform_smat | transform a matrix (center/scaling; truncation; clustering;)... |
| truncByLimit | truncate a matrix by limit |
| truncByQuantile | truncate a matrix by quantile |
| truncMat | truncate matrix used to generate heatmap; add option to scale |
| ttestP | Compute t test P value |
| updatePal | update color pal (as input for prepcolbar) |
| vec2colvec | convert a character vector to a color vector by specified... |
| venndiagram | Generic venndiagram method |
| venndiagram.rowTWanovaMatVec | venndiagram method for rowTWanovaMatVec class |
| whichCat | which columns are categorical |
| whichCont | which columns of a data frame is continuous (numeric) |
| wilcoxP | wilcox P value for a vector of response and a vector of group |
| write.csvOR | write csv with overwrite option |
| WriteXLS_arrayOR | write xls (using WriteXLS) with overwrite option from an... |
| WriteXLS_listOR | write xls (using WriteXLS) with overwrite option from a list |
| WriteXLSOR | write xls (using WriteXLS) with overwrite option |
