Dmitry Grapov dgrapov
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| #test | |
| test<-function(){print("hello world!")} |
dgrapov
/ plotting power calculations
Last active
December 11, 2015 05:48
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| #purpose: model the relationship between effects size, sample size and power | |
| # holding the significance level constant (p = 0.05) for three of the most common statistical tests: | |
| # 1) t-Test (two-sample) | |
| # then visualize the results for medium small, medium and large effect sizes (0.2,0.5,0.8 ; http://www.uccs.edu/lbecker/effect-size.html) | |
| #Need pwr package | |
| if(!require(pwr)){install.packages("pwr");library("pwr")} | |
| # t-TEST |
dgrapov
/ load devium.r
Last active
December 11, 2015 16:28
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| #load devium (or any other package) from github repo | |
| source.git.hub<-function(url = "https://github.com/dgrapov/devium/tree/master/R") | |
| { | |
| if(require(RCurl)==FALSE){install.packages("RCurl");library(RCurl)} else { library(RCurl)} | |
| #get the names of all scripts to source | |
| obj<-getURL("https://github.com/dgrapov/devium/tree/master/R",ssl.verifypeer=FALSE) | |
| tmp<-strsplit(obj,'href=\"/') | |
| tmp2<-unlist(strsplit(as.character(unlist(tmp)),'class')) | |
| scripts<-gsub("/blob","",gsub('\" ',"",tmp2[grep("dgrapov/devium/blob/master/R/",tmp2)])) # fix formatting |
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| 689043 C01197 | |
| 6443013 C14762 | |
| 6443013 C14762 | |
| 6446027 C14765 | |
| 6446027 C14765 | |
| 11954058 C14813 | |
| 6439873 C16326 | |
| 6439873 C16326 | |
| 1004 C00009 | |
| 1023 C00013 |
dgrapov
/ KEGG reaction pairs
Last active
December 13, 2015 19:39
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| C00005 C00006 | |
| C00003 C00004 | |
| C00002 C00008 | |
| C00019 C00021 | |
| C00007 C00027 | |
| C00010 C00024 | |
| C00002 C00020 | |
| C00002 C00013 | |
| C00002 C00009 | |
| C00015 C00029 |
dgrapov
/ CID to inChi Key
Last active
December 13, 2015 20:09
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| 19 GLDQAMYCGOIJDV-UHFFFAOYSA-N | |
| 36 RNQHMTFBUSSBJQ-UHFFFAOYSA-N | |
| 45 ROBFUDYVXSDBQM-UHFFFAOYSA-N | |
| 49 QHKABHOOEWYVLI-UHFFFAOYSA-N | |
| 51 KPGXRSRHYNQIFN-UHFFFAOYSA-N | |
| 58 TYEYBOSBBBHJIV-UHFFFAOYSA-N | |
| 70 BKAJNAXTPSGJCU-UHFFFAOYSA-N | |
| 71 FGSBNBBHOZHUBO-UHFFFAOYSA-N | |
| 72 YQUVCSBJEUQKSH-UHFFFAOYSA-N | |
| 76 FMGSKLZLMKYGDP-UHFFFAOYSA-N |
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| InChI=1S/C7H6O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,8-9H,(H,10,11) | |
| InChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12) | |
| InChI=1S/C3H4O5/c4-1(2(5)6)3(7)8/h1,4H,(H,5,6)(H,7,8) | |
| InChI=1S/C5H8O3/c1-3(2)4(6)5(7)8/h3H,1-2H3,(H,7,8) | |
| InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10) | |
| InChI=1S/C4H6O3/c1-2-3(5)4(6)7/h2H2,1H3,(H,6,7) | |
| InChI=1S/C6H10O3/c1-4(2)3-5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9) | |
| InChI=1S/C6H8O5/c7-4(6(10)11)2-1-3-5(8)9/h1-3H2,(H,8,9)(H,10,11) | |
| InChI=1S/C7H6O4/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3,8-9H,(H,10,11) | |
| InChI=1S/C19H28O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h3,13-16,20H,4-11H2,1-2H3 |
dgrapov
/ Orthogonal Signal Correction (OSC) for PLS models OSC-PLS (OPLS)
Last active
November 28, 2023 03:28
Orthogonal Signal Correction for PLS models (OPLS)
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| #see updated code base and some examples in the function "test" | |
| # https://github.com/dgrapov/devium/blob/master/R/Devium%20PLS%20%20and%20OPLS.r | |
| #Orthogonal Signal Correction for PLS models (OPLS) | |
| #adapted from an example in the book <a href="http://www.springer.com/life+sciences/systems+biology+an+bioinfomatics/book/978-3-642-17840-5">"Chemometrics with R by Ron Wehrens"</a> | |
| #this code requires the following packages: | |
| need.packages<-c("pls", # to generate PLS models | |
| "ggplot2" ) # to plot results |
dgrapov
/ metabolomic network.R
Last active
December 15, 2015 18:49
Tutorial code for making edge lists for biochemical and chemical similarity networks
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| #load needed functions: R package in progress - "devium", which is stored on github | |
| source("http://pastebin.com/raw.php?i=Y0YYEBia") | |
| # get sample chemical identifiers here:https://docs.google.com/spreadsheet/ccc?key=0Ap1AEMfo-fh9dFZSSm5WSHlqMC1QdkNMWFZCeWdVbEE#gid=1 | |
| #Pubchem CIDs = cids | |
| cids # overview | |
| nrow(cids) # how many | |
| str(cids) # structure, wan't numeric | |
| cids<-as.numeric(as.character(unlist(cids))) # hack to break factor |
dgrapov
/ max intensity mass to charge pair.r
Created
April 4, 2013 21:52
Data processing script to get maximum m/z ion intensity pair from Agilent recursive analysis
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| #directory (file path) where the file is | |
| #note make sure all \ are changed to \\ or / | |
| dir<-"ZZZ" | |
| setwd(dir) # change directory | |
| #name of file, should be .csv | |
| file.name<-"XXX.csv" | |
| #load data into R this assumes there is a header | |
| input<-read.csv(file.name, header = TRUE) |
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