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 <[email protected]> On Behalf Of Spencer Brackett
Sent: February 14, 2019 12:32 AM
To: R-help <[email protected]>; Sarah Goslee <[email protected]>;
Caitlin Gibbons <[email protected]>; Jeff Newmiller
<[email protected]>
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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______________________________________________
[email protected] mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
