Man pages for htc502/ewrefxn
this package collects r fxns useful in my daily coding life
| affy.ivt.prep | affymatrix ivt microarray preprocessing 'lite' version |
| affy.Microarray.preprocessing | internal fxn for affymatrix IVT microarray preprocessing |
| affy.st.prep | affymatrix tilling microarray preprocessing |
| agilent44k.prep | agilent 4*44k microarray raw data preprocessing |
| batchedRP | calculate DEGs considering additional factors, using Rankprod |
| batchedRP_filter | filter batchedRP DEG based on fold change and fdr |
| bigcorXY | correlation on big matrix |
| biocInst | install a package using bioconductor |
| combineHTseq | combine htseq count result into a matrix |
| datPrep | internal fxn for array data preprocessing |
| diffCalc | internal fxn for array data DEG calc |
| diffOutput | internal fxn for thresholding and output DE result |
| diskEaten | find the extraordinary large directories under the given dir |
| ebi.affy.ivt.prep | function to processing affymetrix ivt chip data(exon chip) |
| ebi.affy.st.prep | preprocessing affymetrix chip data |
| ebi.agilent44k.prep | function to process agilent44k chip data this function is... |
| ebi.agilent80k.prep | function to process agilent80k chip data this function... |
| ebi.fetch | fetch gene expression data from EBI arrayexpress |
| enrich.test | fisher's exact test and hypergeometric test for gene set |
| ewrefxn | ewrefxn. |
| fc.calc | fc.calc for small sample DEG identification based on FC |
| findfactors | prime decomposition |
| gassigSearch | tackling with exon array gene annotation |
| genepix.prep | genepix array preprocessing(experimentail) |
| geo.agilent44k.prep | agilent 4*44k microchip preprocessing method |
| geo.agilent80k.prep | agilent 4*44k microchip preprocessing method |
| getMeta | phenotype data extractor of an geoquery object |
| getMtr | matrix extractor of an geoquery object |
| getSYMBLgpl | get symbol from ncbi geo GPL table |
| grpFactor | 'combine' multiple factors |
| gsea.gmt.outputMatrix | output with each pathway as a column |
| gsea.gmt.reOrganize | re-organize the list returned by read.gsea.gmt |
| gseaHeatmap | Make heatmap based on gsea enrichment results |
| human2mouse | map gene symbols between mouse and human |
| ilumi.preprocess | internal fxn for illumina microarray preprocessing |
| is.installed | check if a package has been installed or not |
| list2matrix | A list to matrix transform function |
| list2OccTable | convert a named list to an Ocurrence table(emerged 1, absent... |
| list2OccTable1 | convert a named list to an Ocurrence table(emerged 1, absent... |
| list2table | rearrange degs.list to degs table |
| maxlen | internal fxn used in list2matrix |
| mouse2human | map gene symbols between mouse and human |
| myVennDiagram | VennDiagam with color and font set |
| nimblegene.prep | nimblegene array preprocessing(experimentail) |
| read.gsea.gmt | read in gmt gene set file from gsea |
| read.sdrf | readin arrayexpress sdrf file |
| require0 | if hasn't been installed, install and load |
| rm.absent | function used to filter expression matrix based on detection... |
| sameOrder | Check if two character vectors has the same element order |
| searchNCBI | search NCBI pubmed for wanderful papers |
| soft2exp | expression matrix generator |
| soft2exp.pval | expression matrix generator (with detection pvalue) |
| tbl2hmap | convert long tibble to pheatmap data input |
| whichmaxlen | internal fxn |
