Genomic Analysis

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 |

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