Thursday, November 29, 2018

Run R code in command line



# R -f ms02_driver_20180523.R --args bg.phys.csv bg.3.csv 100 0.025 9 > log.3.txt



https://stackoverflow.com/questions/18306362/run-r-script-from-command-line

convert Rmd to R code, knitr


http://felixfan.github.io/extract-r-code/

purl("test.Rmd")

Tuesday, November 20, 2018

Monday, November 19, 2018

Biocarta


http://amp.pharm.mssm.edu/Harmonizome/about

data sets for MS02 manusciipt

Standard data sets for enrichment test by Li, Wei, Genes 2017, pathway enrichent analysis with networks (random walk)



NCBI GEO Potential data sets with GEO2R

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50864

  • Gong Y, Zack TI, Morris LG, Lin K et al. 
    Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. Nat Genet 2014 Jun;46(6):588-94. PMID: 24793136

Tuesday, November 13, 2018

mini autoclave


https://www.laboratory-equipment.com/laboratory-equipment/bioclave-autoclaves.php

biosafety hood

https://www.terrauniversal.com/product/1688-92A-48

Cat #DescriptionQty$/EachTotal
1688-92A-48Hood; 48"W x 30"D, ValuLine WhisperFlow, Vertical Laminar Flow, 120V1$2,187.00$2,187.00
Total:$2,187.00
This hood is 48" W x 30" D x 41" H

This should work with OT2 opentron, whose dimension is width 63cm, depth 57cm, height 66cm.


Wednesday, November 7, 2018

Respondus personality change

Respondus personablity refer to blackboards, canvas, moodle etc.

This can be changed in start settting.

NetBAS running time problem, yeast PIN, GOBP ~ GOBP 4.2 hours


The following codes run for 4.2 hours on applejack laptop using single core.  Need to use parallel method to speed this up. 

```{r}
pairsBuffer = data.frame(matrix(NA, nrow = 1, ncol=3))
names(pairsBuffer) = c("name1", "name2", "tag")
for ( i in 1:length(pairs[,1])){
  print(i)
  #els1 = sort( unlist( strsplit(  pairs$cat1[i], split=",") ))
  #els2 = sort( unlist( strsplit(  pairs$cat2[i], split=",") ))
  sub1 = cats[ cats$id == pairs$name1[i], ]
  sub2 = cats[ cats$id == pairs$name2[i], ]
   
  tagbuffer = allCombinationsOfTwoVectors ( sub1$GO, sub2$GO)  #all combinations
 
  # generate a dataframe buffer with ids
  currentBuffer = data.frame( cbind(rep(pairs$name1[i], length(tagbuffer)),
                        rep(pairs$name2[i], length(tagbuffer)),
                        tagbuffer                        ))
  names(currentBuffer) = c("name1", "name2", "tag")
 
  pairsBuffer = rbind( pairsBuffer, currentBuffer) #combine with dataframe buffer
}

F.obs = data.frame( table(pairsBuffer$tag))
names(F.obs) = c("tag", "freq")
F.obs

Thursday, November 1, 2018

yeast PIN ms02 Zscore map


An interesting curve was seen. Only 2 ms02 null were used in this plot.