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View test.r
#test
test<-function(){print("hello world!")}
View plotting power calculations
#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
View load devium.r
#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
@dgrapov
dgrapov / CID_KEGG pairs
Last active Dec 13, 2015
CID_KEGG pairs
View CID_KEGG pairs
689043 C01197
6443013 C14762
6443013 C14762
6446027 C14765
6446027 C14765
11954058 C14813
6439873 C16326
6439873 C16326
1004 C00009
1023 C00013
View KEGG reaction pairs
C00005 C00006
C00003 C00004
C00002 C00008
C00019 C00021
C00007 C00027
C00010 C00024
C00002 C00020
C00002 C00013
C00002 C00009
C00015 C00029
View CID to inChi Key
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
View inchi code
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
dgrapov / Orthogonal Signal Correction (OSC) for PLS models OSC-PLS (OPLS)
Last active Mar 22, 2019
Orthogonal Signal Correction for PLS models (OPLS)
View Orthogonal Signal Correction (OSC) for PLS models OSC-PLS (OPLS)
#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
dgrapov / metabolomic network.R
Last active Dec 15, 2015
Tutorial code for making edge lists for biochemical and chemical similarity networks
View metabolomic network.R
#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
dgrapov / max intensity mass to charge pair.r
Created Apr 4, 2013
Data processing script to get maximum m/z ion intensity pair from Agilent recursive analysis
View max intensity mass to charge pair.r
#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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