Contrasting data in R - r
I'm trying to draw contrasts. I've used the following script
contrast <- makeContrasts(tam=("GSM151013-GSM150949"), ("GSM151014-GSM150950"), ("GSM151016-GSM150951"), ("GSM151019-GSM150953"), ("GSM151025-GSM150954"),levels=design)
'design' is as follows
tam tamless
GSM151013 0 1
GSM151014 0 1
GSM151016 0 1
GSM151019 0 1
GSM151025 0 1
GSM150949 1 0
GSM150950 1 0
GSM150951 1 0
GSM150953 1 0
GSM150954 1 0
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$f
[1] "contr.treatment"
when I run the code I receive the following error:
Error in eval(ej, envir = levelsenv) : object 'GSM151013' not found
Any help would be appreciated
You might have syntax problem.
Try this:
design <- c('GSM151013', 'GSM150949', 'GSM151014', 'GSM150950',
'GSM151016', 'GSM150951', 'GSM151019', 'GSM150953',
'GSM151025', 'GSM150954')
makeContrasts(GSM151013-GSM150949, GSM151014-GSM150950, GSM151016-GSM150951,
GSM151019-GSM150953, GSM151025-GSM150954, levels=design)
Related
How can I pull player stats from a tabbed ESPN table?
I've been reading through a couple of the other useful guides on pulling player and match data from ESPN using R, however I have come across a problem with tabbed tables. As shown here on the player stats for a recent rugby game, the player statistics table is tabbed into 'Scoring', 'Attacking', 'Defending' and 'Discipline'.
Using the following code (with the help of two lovely packages (RCurl and htmltab), I can pull out the first tab ('Scoring') from that page ...
# install & attach RCurl
if (!base::require(package="RCurl")) utils::install.packages("RCurl")
library(RCurl)
# install & attach htmltab
if (!base::require(package="htmltab")) utils::install.packages("htmltab")
library(htmltab)
# assign URL
theurl <- RCurl::getURL("https://www.espn.co.uk/rugby/playerstats?gameId=294854&league=270557",.opts = list(ssl.verifypeer = FALSE))
# pull tables from url
team1 <- htmltab::htmltab(theurl,which=1)
team2 <- htmltab::htmltab(theurl,which=2)
league <- htmltab::htmltab(theurl,which=3)
... in the following format, which is exactly what I wanted ...
team1
rowID LEINS Tx TA CG PG PTS
2 J LarmourFB 0 0 0 0 0 0
3 H KeenanW 0 0 0 0 0 0
4 G RingroseC 0 0 0 0 0 0
5 R HenshawC 1 0 0 0 0 5
6 J LoweW 1 0 0 0 0 5
7 R ByrneFH 0 0 2 2 0 10
8 J Gibson-ParkSH 0 1 0 0 0 0
9 C HealyP 0 0 0 0 0 0
10 R KelleherH 0 0 0 0 0 0
11 A PorterP 0 0 0 0 0 0
... however I seem unable to pull out any tab other than 'Scoring'. I'm sure I'm missing something really obvious, so would appreciate someone pointing out where I'm going wrong!
Thanks in advance!
if you check the source html-page you will see that the data is not there at the start. You can find a data-reactid-tag that indicates that the data is only loaded once you click on the new tab. So you will need to find a way to make that click on the second tab. One option for you might be to use Selenium: https://www.rdocumentation.org/packages/RSelenium/versions/1.7.7 This would enable you to make the necessary button click. A sample can be found here: https://www.r-bloggers.com/2014/12/scraping-with-selenium/
how to read a specific .Matrix file in R
I have a .Matrix file, I have been told it is similar to .csv file, and I take a look by web browser, it looks like this:
%TransMat_H0004.E1.L1.S1.B1.T1
CLUSTER,,3,3,2,2,1,1,3,1,1,1,1,3,2,3,1,2,2,1,1,3,3,1,2,1,3,1,1,2,1,3,3,2,3,3,1,1,1,1,1,3,3,1,2,3,2,1,1,1,1,2,1,2,2,3,1,3,2,2,2,1,3,3,2,3,3,1,2,3,3,2,2,2,3,2,2,2,1,1,2,1,1,2,1,1,1,1,2,3,1,3,2,3,3,3,3,2,1,1,3,3,3,1,1,1,2,1,3,1,2,1,1,1,1,1,1,1,3,1,3,2,3,1,1,3,2,2,3,3,1,3,1,1,2,1,2,2,1,1,3,3,1,2,1,2,2,2,2,2,1,3,1,2,3,2,2,2,2,3,2,1,1,2,3,3,2,1,3,1,1,1,1,3,3,3,1,3,3,1,2,2,3,2,3,2,2,3,1,2,2,1,3,1,2,2,3,1,2,3,2,3,3,1,3,2,3,1,1,2,3,1,1,3,2,1,2,1,1,3,1,1,3,1,1,2,1,2,2,2,3,1,3,3,3,1,3,1,1,3,2,3,1,3,2,1,3,1,1,1,2,3,3,3,1,3,3,3,1,1,2,2,3,2,3,3,3,1,3,3,1,1,2,3,2,1,1,3,1,1,1,1,1,3,3,2,2,1,1,1,1,1,3,1,1,2,3,3,1,1,3,2,2,1,1,2,1,1,3,2,1,2,1,2,3,2,1,1,3,2,1,3,2,1,2,2,1,3,3,1,3,3,2,3,2,3,1,3,3,3,3,2,1,3,2,3,3,3,2,1,2,1,2,3,1,1,3,3,3,3,3,2,3,3,1,3,1,1,2,3,3,3,3,3,3,2,2,2,3,1,2,3,3,3,3,2,1,2,2,3,2,3,2,3,2,3,3,2,1,2,3,3,2,1,2,3,3,3,1,3,2,3,3,1,2,2,3,1,1,2,2,3,2,1,1,2,2,1,3,1,2,3,1,3,1,1,2,3,3,1,2,3,2,2,1,1,2,3,2,2,2,1,2,1,2,2,3,2,1,2,1,3,1,2,3,1,2,3,1,2,1,1,2,1,3,3,3,1,3,3,2,2,2,1,2,3,1,3,1,2,1,3,1,2,2,1,2,3,1,1,3,3,2,2,3,1,1,2,1,1,1,2,1,2,3,3,2,2,1,2,3,2,3,1,2,2,2,1,3,3,3,3,3,3,2,3,2,1,2,1,3,3,1,3,3,1,3,2,3,3,1,2,3,3,3,3,3,1,2,1,2,1,1,1,1,2,2,3,1,1,2,3,2,3,2,2,3,3,1,2,1,3,2,3,2,2,3,2,3,1,1,1,3,1,2,3,1,3,2,3,2,2,1,2,3,1,3,2,1,2,3,1,3,1,2,2,1,3,3,2,1,3,3,1,2,3,1,2,1,1,3,1,3,2,3,3,3,3,2,2,1,1,3,3,2,1,3,1,1,3,3,3,1,3,3,1,1,3,3,3,1,1,3,3,2,1,3,2,3,1,3,2,2,2,2,2,3,3,1,2,2,3,2,3,3,1,3,1,3,3,1,3,2,1,2,3,1,3,1,3,2,2,1,1,1,1,3,2,3,3,2,2,3,2,3,1,3,2,1,2,3,1,2,2,1,1,1,3,3,2,3,3,3,3,2,3,1,1,3,3,3,1,1,3,2,1,2,3,2,3,1,3,3,2,1,1,1,1,3,3,2,3,1,2,1,3,3,3,2,2,2,2,3,3,1,1,2,3,2,2,3,3,2,2,3,3,3,2,2,1,2,2,3,3,3,3,1,2,2,3,2,2,2,2,3,2,2,2,1,1,2,2,2,1,2,3,2,2,3,3,2,1,3,1,2,2,1,3,2,3,1,1,3,1,2,2,2,3,3,1,3,3,1,2,1,2,3,1,3,2,3,1,1,3,3,3,1,2,3,3,3,1,3,3,1,3,2,2,2,3,2,1,2,3,3,2,1,2,1,2,1,1,3,3,1,1,3,2,1,3,2,1,3,3,3,2,2,2,1,3,2,3,2,3,1,2,3,1,3,3,1,1,3,2,1,2,3,2,1,1,2,3,1,3,2,1,2,2,3,2,2,1,3,2,1,1,3,3,2,1,3,1,2,2,1,2,2,3,2,2,2,3,1,1,3,3,3,3,1,2,2,3,3,3,2,1,3,2,1,2,3,3,1,3,2,1,2,1,1,2,2,3,2,2,3,1,2,3,2,3,1,2,3,3,2,3,3,1,1,2,1,1,1,3,1,3,1,3,3,2,3,1,2,2,1,2,3,3,2,3,2,3,2,1,1,3,2,3,2,3,1,1,3,1,3,2,1,3,2,2,2,3,1,1,2,3,1,1,1,2,3,3,3,1,2,3,3,3,3,2,3,1,3,1,3,2,3,2,3,3,1,1,2,3,1,1,3,3,2,3,3,1,2,3,1,2,3,3,2,3,3,2,1,2,3,3,2,3,1,2,2,3,1,2,1,3,2,3,1,2,2,3,3,2,2,3,1,3,3,3,3,2,3,2,2,1,3,1,2,1,1,1,3,2,3,1,1,1,1,3,3,2,3,1,1,2,1,3,1,2,3,3,2,2,1,1,3,2,2,3,1,2,3,3,3,2,1,2,2,3,1,3,3,2,1,2,2,3,3,2,2,3,2,1,1,3,1,3,3,1,3,2,3,3,3,1,1,1,3,1,2,2,3,2,3,2,3,1,1,2,1,2,1,3,3,1,3,3,2,2,1,3,1,2,2,3,2,2,2,3,3,2,1,1,1,1,3,1,1,2,1,2,2,3,3,2,3,3,3,2,1,1,3,2,2,2,3,1,3,3,3,2,2,3,1,3,3,3,1,3,3,3,2,3,1,2,1,1,3,1,2,3,2,1,3,3,2,1,3,2,3,2,3,1,2,2,3,3,2,3,3,3,1,2,3,3,3,3,3,1,1,2,3,1,2,1,1,1,1,2,1,1,2,3,1,3,3,2,2,3,2,2,1,3,2,2,3,1,1,1,1,1,3,1,3,1,1,3,2,2,3,3,3,1,2,2,3,3,2,3,2,3,3,2,1,2,3,3,1,3,1,2,1,1,2,2,2,2,2,2,1,3,1,3,2,3,2,2,2,2,2,3,2,2,1,3,1,1,1,2,1,2,1,2,1,3,1,3,3,1,3,1,3,3,1,3,2,3,3,3,3,1,3,3,2,3,2,3,3,3,1,1,2,2,3,3,3,2,2,3,3,1,3,1,2,1,2,2,1,1,3,3,1,1,3,1,1,1,2,2,3,2,2,2,3,3,1,2,1,2,2,2,3,2,2,1,2,1,1,1,3,3,3,2,1,3,3,3,2,2,3,1,2,1,3,1,3,3,1,3,2,3,2,2,1,1,1,3,3,2,3,1,3,2,2,2,2,2,3,1,3,2,3,1,3,1,3,1,2,3,2,2,3,3,3,3,3,1,1,2,3,3,2,3,1,3,3,1,3,3,2,2,1,3,3,3,3,2,1,3,2,2,2,3,3,1,1,3,3,3,1,3,1,1,2,3,1,3,3,3,2,1,3,1,2,1,3,2,2,3,1,3,1,2,3,3,3,2,2,3,1,2,1,1,1,2,3,1,2,3,2,3,3,2,1,1,2,3,3,1,2,3,1,1,1,3,1,2,3,1,2,3,2,2,3,2,3,2,3,1,2,3,3,1,3,3,2,2,1,1,2,3,2,2,3,3,2,1,1,1,3,3,3,2,2,1,3,2,2,1,3,2,3,3,1,1,3,2,3,3,2,3,1,3,3,1,3,3,2,3,3,2,3,1,3,3,3,3,3,1,1,3,2,2,3,3,3,3,1,1,1,1,3,2,3,3,1,3,2,2,1,1,1,1,3,2,2,3,2,2,3,3,2,3,1,1,1,3,3,3,3,2,3,1,3,3,1,1,3,3,1,3,3,3,1,3,2,1,1,3,3,2,3,3,3,2,2,1,3,3,3,1,2,2,2,2,1,2,2,1,2,3,2,1,2,2,3,3,3,3,3,2,2,3,2,2,3,2,1,3,1,1,2,2,3,1,2,3,2,1,3,1,1,2,1,2,2,3,1,2,2,3,3,1,3,2,1,3,3,2,1,3,3,3,1,3,2,3,3,2,3,2,2,3,2,1,3,3,3,3,2,1,3,3,3,1,3,3,1,3,1,3,3,3
tSNE-1,,8.13846968090103,12.8635212043927,10.3864480425066,7.17083119797853,-72.7452686458686,-49.7960088439495,45.63460621346,-50.3693843293848,-53.2415432674881,-54.6891175204711,-46.4635164735514,4.49644447816871,3.98243750756555,-9.99729157677144,-98.1041739031645,14.4129117311442,21.8090838800674,-46.5547640077783,-65.8379505581324,39.8907136841164,45.2453417297103,-43.4054353275594,5.58370171555427,-82.6419520577671,42.7647608862027,-91.125151907502,-37.9838559192307,62.9924569510685,-69.108888726706,62.7774653919852,60.3873481045592,62.825
I tried to read it by read.csv:
test=read.csv('TransMat_H0004.E1.L1.S1.B1.T1.Matrix',sep='' )
str(test)
'data.frame': 33141 obs. of 1 variable:
$ X.TransMat_H0004.E1.L1.S1.B1.T1: Factor w/ 33141 levels "A1BG,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"| truncated,..: 13453 31099 31100 1 2 3 4 5 6 7 ...
how should I read it in a right format, say, first character of 'sequence'(list?I guess?) as rowname.
Thanks in advance!
sorry, I cannot provide the data link because it is unpublished; but I can tell you what the data look like:
%TransMat_H0004.E1.L1.S1.B1.T1
cluster,1,2,3,2,3….
tsne-
1,-41,-80…..
tsne-
2,-41,-80…..
tsne-
3,-41,-80…..
(and the rest are all started with gene name and number, such as)
genea, 0,2,1,0…
….
genez,0,2,1,0
my desired output is to remove the first 4 factors(cluster, tsne-1, tsne-2,tsne-3), and extract the gene transcripts matrix,such as:
V1 V2 V3 V4 V5
1 0 0 0 0 0
2 0 0 0 0 0
3 0 0 0 0 0
4 0 0 0 0 0
5 0 0 0 0 0
I figure this out by this:
read.csv("E2.Matrix", skip=1)
since the first row is annotation according to the bioinfor technician who arranged the .Matrix file
Thanks! # Stephan
Error return by R predict function or underlying Rcpp
I apparently have successively used a newer R package called milr, multiple instance logistic regression. Admittedly, I do not make any claims regarding the goodness of the model. However, when I try to use the model to predict I get the error Error in logit(cbind(1, newdata), .) : not compatible with requested type when I call predict as follows: miltp <- predict(milt, SQFM.te, SQFM.teb, type="bag") and miltp <- predict(milt, SQFM.te, SQFM.teb) However I get a NULL return when I call it as: miltp <- predict(milt, SQFM.te, SQFM.teb, type="response") and miltp <- predict(milt, SQFM.te, SQFM.teb, type="class") I have tried using factors, integers and numerics, I am perplexed. My online search only yielded Rcpp: Error: not compatible with requested type which is not helpful for me as R and C++ is over my head. All comments are appreciated, some input info is given below I have tried some conversions str(SQFM.te) 'data.frame': 100369 obs. of 5 variables: $ arstmade: int 0 0 0 0 0 0 0 0 0 0 ... $ perstop : int 0 0 0 0 0 0 0 0 0 0 ... $ trhsloc : int 0 0 0 0 0 0 0 0 0 0 ... $ acrept : int 0 0 0 0 0 0 0 0 0 0 ... $ radio : int 1 1 1 1 1 1 1 1 1 1 ... str(SQFM.teb) int [1:100369] 3 3 3 3 3 3 3 3 3 3 ... print(milt) Coefficients: intercept arstmade perstop trhsloc acrept radio -1.69306 -0.09544 -7.95369 -0.53375 0.16506 -0.61778 Residual Deviance: Inf BIC: Inf
How to remove the csep/non-numeric error while generating heat map in R
I have a data that looks like this:
Cluster_Combined Cluster_1 Cluster_2 Cluster_3 Cluster_4 Cluster_6 Cluster_10
G-protein coupled receptor signaling pathway (15) 2 6 0 4 3 1 0
GTP catabolic process (69) 1 0 0 0 2 0 0
activin receptor signaling pathway (17) 0 2 0 0 0 0 0
acute inflammatory response (7) 2 1 0 0 1 0 0
acute-phase response (8) 5 2 1 0 2 0 0
aging (5) 2 1 2 0 1 0 1
Which I want to create the heat map, based on the values above, where columns refer to the cluster name and row the ontology terms.
Now I have the code below
library(gplots);
dat <- read.table("http://dpaste.com/1505883/plain/",sep="\t",header=T);
hmcols <- rev(redgreen(2750));
heatmap.2(as.matrix(dat),scale="row",cols=hmcols,trace="none",dendrogram="none",keysize=1);
Although it does generate the plot, it gave me the following error:
Error in csep + 0.5 : non-numeric argument to binary operator
Furthermore, I cannot see the red-green effect in the plot.
How can I remove the error?
There is no "cols=" argument to heatmap.2(...). Try col=hmcols. heatmap.2(as.matrix(dat),scale="row",col=hmcols,trace="none",dendrogram="none",keysize=1)
using graph.adjacency() in R
I have a sample code in R as follows: library(igraph) rm(list=ls()) dat=read.csv(file.choose(),header=TRUE,row.names=1,check.names=T) # read .csv file m=as.matrix(dat) net=graph.adjacency(adjmatrix=m,mode="undirected",weighted=TRUE,diag=FALSE) where I used csv file as input which contain following data: 23732 23778 23824 23871 58009 58098 58256 23732 0 8 0 1 0 10 0 23778 8 0 1 15 0 1 0 23824 0 1 0 0 0 0 0 23871 1 15 0 0 1 5 0 58009 0 0 0 1 0 7 0 58098 10 1 0 5 7 0 1 58256 0 0 0 0 0 1 0 After this I used following command to check weight values: E(net)$weight Expected output is somewhat like this: > E(net)$weight [1] 8 1 10 1 15 1 1 5 7 1 But I'm getting weird values (and every time different): > E(net)$weight [1] 2.121996e-314 2.121996e-313 1.697597e-313 1.291034e-57 1.273197e-312 5.092790e-313 2.121996e-314 2.121996e-314 6.320627e-316 2.121996e-314 1.273197e-312 2.121996e-313 [13] 8.026755e-316 9.734900e-72 1.273197e-312 8.027076e-316 6.320491e-316 8.190221e-316 5.092790e-313 1.968065e-62 6.358638e-316 I'm unable to find where and what I am doing wrong? Please help me to get the correct expected result and also please tell me why is this weird output and that too every time different when I run it.?? Thanks, Nitin
Just a small working example below, much clearer than CSV input.
library('igraph');
adjm1<-matrix(sample(0:1,100,replace=TRUE,prob=c(0.9,01)),nc=10);
g1<-graph.adjacency(adjm1);
plot(g1)
P.s. ?graph.adjacency has a lot of good examples (remember to run library('igraph')).
Related threads
Creating co-occurrence matrix
Co-occurrence matrix using SAC?
The problem seems to be due to the data-type of the matrix elements. graph.adjacency expects elements of type numeric. Not sure if its a bug. After you do, m <- as.matrix(dat) set its mode to numeric by: mode(m) <- "numeric" And then do: net <- graph.adjacency(m, mode = "undirected", weighted = TRUE, diag = FALSE) > E(net)$weight [1] 8 1 10 1 15 1 1 5 7 1