Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision |
how_to [2020/01/21 20:50] – [Set the default width of fill mode (line length) in emacs?] admin | how_to [2020/01/22 16:53] – [Read and write excel files in R] isha |
---|
| |
---- | ---- |
| |
| ==== Read and write excel files in R ==== |
| |
| Use [[https://cran.r-project.org/web/packages/openxlsx/index.html|openxlsx]] package to read, write and edit xlsx files in R. Package's integration with C++ makes it faster and easier to use. Simplifies the creation of Excel .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of 'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages with the added benefit of removing the dependency on Java. |
| |
| <code> |
| E.g. Writing four dataframes in four sheets of excel workbook can be done as follows: |
| library(openxlsx) |
| listDataFrames <- list("GO-BP"=data.frame(egoBP), "GO-MF"=data.frame(egoMF), |
| "KEGG" = data.frame(eKEGG), "NCG" = data.frame(ncg)) |
| xlsFile <- file.path(resultPath, paste0(l1, "_ORA_results.xlsx")) |
| write.xlsx(x=listDataFrames, file=xlsFile) |
| </code> |
| |
| ---- |
| |
| |
==== Set local mirror for Rscript ==== | ==== Set local mirror for Rscript ==== |
---- | ---- |
| |
**Convert gene or protein IDs?** \\ | ===== Convert gene or protein IDs? ===== |
[[https://www.biostars.org/p/22/|Use]] [[https://biodbnet-abcc.ncifcrf.gov/db/db2db.php|bioDBnet]], BioMart - Ensembl, or [[https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html|AnnotationDbi]] package in R to convert between Entrez Gene, RefSeq, Ensemble, and many more. | [[https://www.biostars.org/p/22/|Use]] [[https://biodbnet-abcc.ncifcrf.gov/db/db2db.php|bioDBnet]], BioMart - Ensembl, or [[https://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html|AnnotationDbi]] package in R to convert between Entrez Gene, RefSeq, Ensemble, and many more. |
| |
---- | ---- |
| |
| |
===== Prepare attractive, scientific presentations ? ===== | ===== Prepare attractive, scientific presentations ? ===== |
| |
Logitech Control Center may help on the [[https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X|Logitech]] MX mice older than 2019. | Logitech Control Center may help on the [[https://support.logi.com/hc/en-gb/articles/360025297833-Logitech-Control-Center-for-Macintosh-OS-X|Logitech]] MX mice older than 2019. |
| |
| ---- |
| |
| ===== Choose a solid state (SSD) external drive? ===== |
| |
| The non-volatile memory express (NVMe) devices are [[https://ssd.borecraft.com/SSD_Buying_Guide_List.pdf|better]] than SATA solid state drives. Good brands include [[https://smile.amazon.com/gp/product/B07X6CKHH1/ref=ox_sc_act_title_1?smid=A29Y8OP2GPR7PE&psc=1|Sabrent]] (Nano is smaller than Pro but gets hot when extensivly used), Seagete, Addlink, and Team. As of 2020, a speed of 1000 Mb/s is possible using USB 3.2. |
| |
| ---- |
| |
| |