[R] R Data

[Fowler, Mark]

Hi Spencer,

The an1 syntax is adding regression coefficients (or NAs where a regression could not be done) to the downloaded and processed data, which ends up a matrix. The cbind function adds the regression coefficients to the last column of the matrix (i.e. bind the columns of the inputs in the order given). Simple example below. Not actually any need for the separate cbind commands, could have just used an1=cbind(an,p,t). The cbind function expects all the columns to be of the same length, hence the use of the tryCatch function to capture NA's for failed regression attempts, ensuring that p and t correspond row by row with the matrix.

 x=seq(1,5)
 y=seq(6,10)
 z=seq(1,5)
xyz=cbind(x,y,z)
xyz
   x  y z
[1,] 1  6 1
[2,] 2  7 2
[3,] 3  8 3
[4,] 4  9 4
[5,] 5 10 5
dangs=rep(NA,5)
xyzd=cbind(xyz,dangs)
xyzd
     x  y z dangs
[1,] 1  6 1    NA
[2,] 2  7 2    NA
[3,] 3  8 3    NA
[4,] 4  9 4    NA
[5,] 5 10 5    NA

-----Original Message-----
From: R-help <r-help-bounces using r-project.org> On Behalf Of Spencer Brackett
Sent: February 14, 2019 12:32 AM
To: R-help <r-help using r-project.org>; Sarah Goslee <sarah.goslee using gmail.com>; Caitlin Gibbons <bioprogrammer using gmail.com>; Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
Subject: [R] R Data

Hello everyone,

The following is a portion of coding that a colleague sent. Given my lack of experience in R, I am not quite sure what the significance of the following arguments. Could anyone help me translate? For context, I am aware of the downloading portion of the script... library(data.table) etc., but am not familiar with the portion pertaining to an1 .

library(data.table)
anno = as.data.frame(fread(file =
"/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/450K/mapper.txt", sep ="\t", header = T)) meth = read.table(file = "/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/27K/GBM.txt", sep  ="\t", header = T, row.names = 1) meth = as.matrix(meth) """ the loop just formats the methylation column names to match format"""
colnames(meth) = sapply(colnames(meth), function(i){
  c1 = strsplit(i,split = '.', fixed = T)[[1]]
  c1[4] = paste(strsplit(c1[4],split = "",fixed = T)[[1]][1:2],collapse =
"")
  paste(c1,collapse = ".")
})
exp = read.table(file =
"/rsrch1/bcb/kchen_group/v_mohanty/data/TCGA/RNAseq/GBM.txt", sep = "\t", header = T, row.names = 1) exp = as.matrix(exp) c = intersect(colnames(exp),colnames(meth))
exp = exp[,c]
meth = meth[,c]
m = apply(meth, 1, function(i){
  log2(i/(1-i))
})
m = t(as.matrix(m))
an = anno[anno$probe %in% rownames(m),]
an = an[an$gene %in% rownames(exp),]
an = an[an$location %in% c("TSS200","TSS1500"),]

p = apply(an,1,function(i){
  tryCatch(summary(lm(exp[as.character(i[2]),] ~ m[as.character(i[1]),]))$coefficient[2,4], error= function(e)NA)
})
t = apply(an,1,function(i){
  tryCatch(summary(lm(exp[as.character(i[2]),] ~ m[as.character(i[1]),]))$coefficient[2,3], error= function(e)NA)
})
an1 =cbind(an,p)
an1 = cbind(an1,t)
an1$q = p.adjust(as.numeric(an1$p))
summary(lm(exp["MAOB",] ~ m["cg00121904",]$coefficient[2,c(3:4)]
###############################################

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