Man pages for nickytong/GenAnalysis
Genomic Analysis

aheatmapA function to draw clustered heatmaps.
aheatmap2a wrapper to aheatmap which enables passing phenoData. This...
aheatmatannotated heatmap using heatmat engine
aheatmatcorplot correlation heatmap for rows from a matrix
aMatrixplot matrix values
anovaPANOVA test P value
aoMatrixplot an ordered (sorted) matrix
augmentMatrixColumnByIDAugment a matrix by ID in the direction of columns
augmentMatrixColumnByID_updateupdate augMat after it is subsetted
augmentMatrixRowByIDAugment a data frame by ID in the direction of rows
autocolpal4DFget default colorpal (color vector) for a data frame...
BootstrapGenesConsensus clustering based on BootstrapClusterTest from OOMPA
buildappbuild an openCPU app with...
buildapp0build an openCPU app with build+install+opencpu$browse
buildSilhouetteextract silhouette information for clustering
categorizePvecconvert P value into categories
cluster_mathierarchical clustering with rows using given distance and...
colorpalette2colvecextracts color given a specified pallete (string) possibly...
combine_cormatwhen pearson and spearman values both are desired, we can fit...
convert_annotationsconvert annotation (data frame) and annotation_colors (a...
cophCorFromConsMatcalculate cophenetic coefficient for a consensus matrix...
copheneticCoefcalculate cophenetic coefficient for a hierarchical...
corTestcorrelation betweent two vector
coxphP2cox PH P value
create_bumCreate a bum 'object'
decideOrder2-step procedure to decide ordering
df_force_factorforce selected columns of a data frame as factor
df_format_dfformat a data frame by imposing non-continuous variables as...
dichotomizeExprdichotomize expression into binary based on BI or quantile
dichotomizeExpr_BIdichotomize expression into binary based on BI
dichotomizeExpr_quantiledichotomize expression into Low/High group
dispersionFromConsMatcalculate dispersion from a consensus matrix extracted from...
doccoRmdgenerate html from Rmd with docco-linear style as in <URL:...
emptydfFromDFthere may be mroe elegant ways to do this
fitSIBERonMatfit SIBER on a matrix, one row at a time
fitSIBERonMat_Bygroupfit SIBER on matrix but split by group
fn_TWanovatwo way anova test for a given response and two vectors
formatAnnotation4aheatmapPrepare annotation data frame so that aheatmap can show it
formatDFformat a data frame using formatVec
formatLevelformatting a given vector according to given levels
formatVecformat a vector by forcing into a factor if not numeric or...
genbreaksgenerate breaks for specified start, end position and n,...
generate_breaksgenerate breaks for an input matrix or vector
generate_breaks0when center=TRUE, the broken bars at 0 has equal length of...
getDefaultBarColListsometimes we just want a default barColList rather than...
getfisherPcompute fisher exact test (chisq test when failure) p value...
get_palobtain color pallete defined in this package
getPvecSmrygiven a p value vector and a vector of cutoffs, find number...
get_stretchcompute stretch from a continuous map
gettergeneral getter function for attributes in an object
getter.augMatget method for class augMat
getter.colpal4DFget method for class colpal4DF
getter.rowanovaMatVecget method for class rowanovaMatVec
getter.rowcorMatVecget method for class rowcorMatVec
getter.rowttestMatVecget method for class rowttestMatVec
getTopNindexget top N elements from a vector and return a vector of index...
getTopNvalueget top N elements from a vector
ggKMplot OS against a continuous variable by breaking the...
ggKMcatfor categorical covariate x, plot KM curve
guessAlphaguess alpha
guessAlpha_lineguess alpha in a line plot
guess_angleguess angle for axis angle
guessCEXgiven number of genes G in a heatmap, guess rowCEX to be...
guess_nrowLguess nrowL from a specified number of categories
heatmGeneric heatm method
heatm.rowcorMatVecHeatmap plot for rowcorMatVec class
heatm.rowttestMatVecHeatmap plot for rowttestMatVec class
hist.rowanovaMatVecBum plot for rowanovaMatVec class
hist.rowcorMatVecBum plot for rowcorMatVec class
hist.rowfisherMatVecBum plot for rowfisherMatVec class
hist.rowpairedttestMatVecBum plot for rowpairedttestMatVec class
hist.rowttestMatVecBum plot for rowttestMatVec class
hist.rowTWanovaMatVecBum plot for rowTWanovaMatVec class
isCatcheck if a vector is categorical or continuous
iscatDFcheck columnwise of a data frame whether it is categorical...
isContindex of columns of a data frame is continuous (numeric)
is_continuousguess if a vector is continuous
isTopNreturn a logical vector if elements in a vector is top N...
ixglobal2localmap global index to local index given reference
ixlocal2globalmap local index to global index given reference
ixunify2indexunify index/name indexing into global index given global name
lm_xylm for cont x and y
logic2sortedIndexconver logic vector to sorted index vector
makeColMatprepare a matrix for plotting by converting it to a color...
makestringimpose as.character
mapNamesmapping a vec to another name space
mapNames4matfor a matrix, i.e. 0, 1, we may want to format it as WT, MUT
maskByLimitmask values as NA in a matrix
mylibrarymultiple scatter plot for a given data frame
namedColVecGenerate a named color vector
name-of-the-vec-as-in-the-named-list-of-colpalbuild a map given a vector of values and color pallete
noNAremove NA cases for either a vector, matrix or data frame
nonNumeric2FactorByColumnforce to factor when non-numeric
n_uniquereturn the number of unique values
overwritefa wrapper for file overwrite
pairedttestPpaired t-test
parse_coxphP2parse the coxphP2() returned value to text so as to show OR,...
pdfORpdf() with overwrite option
plainRmdgenerate html with plain style
plot4rowanovaMatVecordered horizontal bar plot for rowanovaMatVec
plot4rowcorMatVecordered bar plot for rowcorMatVec class
plot4rowttestMatVecordered horizontal bar plot for rowttestMatVec
plotBumFDRplot bum with FDR table on it
plotCatCatplot cat-cat
plotCCCCalculates Concordance Correlation Coefficient (CCC) to...
plot.colpal4DFplot method for colpal4DF
plotContCatplot Cont-Cat variable
plotContContplot Cont-Cont variable
plot.fn_TWanovaPlot method for fits from two-way data by fn_TWanova
plotHeatmappresent a heatmap
plotHeatmapTableplot a table with colour indicated
plotKMflexible KM curve wrapper
plotKM0plot just KM
plotMeanSD4matplot mean vs sd for a matrix for quick QC/filtering
plot.phmplot method for phm class
plot.prepcolbarplot method for prepcolbar class
plot.rowanovaMatVecBar plot for rowanovaMatVec class
plot.rowcorMatVecBar plot for rowcorMatVec class
plot.rowttestMatVecBar plot for rowttestMatVec class
plotScatterflexible scatter plot (a wrapper)
plotSummaryFromConsensusClusterPlusplot the fit from ConsensusClusterPlus()
polrPordinal regression for association between an ordered...
prepare4aheatmapgiven a mat and phenoDat and barColList, calculates...
prepare4ColListgiven a list of barColors and phenoData, prepare a list of...
prepcolbarbuild colmat/colmap given pheno (colwise of data frame) and...
prepDat4pairedttestgiven a vector of data (continuous) and class (binary) and...
print.phmprint method for phm class
printPvecSmrygiven a p value vector and a vector of cutoffs, find number...
rcorrcorr to compute correlation coefficient among columns.
rcorrTestcomputes correlation between two vectors
rowanovaMatVecANOVA between rows of a matrix and a vector
rowcorMatMat_Lextension of rowcorMatVec
rowcorMatVecCalculate correlation between rows of a matrix and a vector
rowcorMatVec_Bygroupthe grouped version for rowcorMatVec
rowdoMatVec_Bygroupthe driver of grouped version calculations, enpowering...
rowfisherMatVecPerform Fisher Exact test between rows of mat (categorical)...
rowkmMatVecPerform log rank test between rows of mat (categorical) and a...
rowlmMatVecFit a linear model with rows of mat and vec, possibly adding...
rowMatVecDoperform operations between rows of a mat and a vector
rowpairedttestMatVecPaired t test between rows of a matrix and a vector
rowranktestMatVeccompute rank test P as well as a t test result
rowttestMatMat_Lextension of rowttestMatVec
rowttestMatVecPerform t test between rows of mat and a vector; Notice...
rowTWanovaMatVecTwo-way ANOVA between rows of a matrix and two vectors: two...
RPPAdatAn example KEGG Gene2Annotation data
safeloglog transformation of matrix, i.e. count matrix
saveORsave() with overwrite option
scale_matscale a matrix by row, by column or none
scatterGeneric scatter method
scatter_rowanovaMatVecscatter plot for rowanovaMatVec
scatter.rowanovaMatVecScatter plot for rowanovaMatVec class: each row produces a...
scatter_rowcorMatVecscatter plot for rowcorMatVec
scatter.rowcorMatVecScatter plot for rowcorMatVec class: each row produces a...
scatter.rowfisherMatVecScatter plot for rowfisherMatVec class: each row produces a...
scatter.rowkmMatVecScatter plot for rowkmMatVec class: each row produces a...
scatter.rowpairedttestMatVecScatter plot for rowpairedttestMatVec class: each row...
scatter_rowttestMatVecScatter plot for rowttestMatVec
scatter.rowttestMatVecScatter plot for rowttestMatVec class: each row produces a...
scatter_rowTWanovaMatVecscatter plot for rowanovaMatVec
scatter.rowTWanovaMatVecScatter plot for rowTWanovaMatVec class: each row produces a...
selectGeneFromMeanSDselect genes based on mean~SD plot from plotMeanSD4mat
SIBER2Compute BI for a gene expression matrix
statContContCalculate statistics for continuous variable x and y
str_extract2extract string given a pattern using back reference...
subsetMainMatsubset main expression mat
s_uniqueunique values sorted
swapswap two variables in a given environment
testObjectTest if an object exist
testreeGeneric testree method (for phm object produced by...
testree.phmtestree method for class phm
test_tree_splittest association between tree cut and a vector
theme_basea theme mimic the base system
toFCgiven expression mean difference, transforms back to fold...
toNaturalVarconvert R variable names (i.e. from read table with default...
transform_smattransform a matrix (center/scaling; truncation; clustering;)...
truncByLimittruncate a matrix by limit
truncByQuantiletruncate a matrix by quantile
truncMattruncate matrix used to generate heatmap; add option to scale
ttestPCompute t test P value
updatePalupdate color pal (as input for prepcolbar)
vec2colvecconvert a character vector to a color vector by specified...
venndiagramGeneric venndiagram method
venndiagram.rowTWanovaMatVecvenndiagram method for rowTWanovaMatVec class
whichCatwhich columns are categorical
whichContwhich columns of a data frame is continuous (numeric)
wilcoxPwilcox P value for a vector of response and a vector of group
write.csvORwrite csv with overwrite option
WriteXLS_arrayORwrite xls (using WriteXLS) with overwrite option from an...
WriteXLS_listORwrite xls (using WriteXLS) with overwrite option from a list
WriteXLSORwrite xls (using WriteXLS) with overwrite option
nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.