Last updated: 2018-05-21

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Here I’m going to try fitting a GP to the cell cycle data:

d = readRDS("../data/cyclegenes.rds")
dim(d)

[1] 990  11

Recall each row is a single cell. The first column (“theta”) is an estimate of where that cell is in the cell cycle, from 0 to 2pi. (Note that we don’t know what stage of the cell cycle each point in the interval corresponds to - so there is no guarantee that 0 is the “start” of the cell cycle. Also, because of the way these data were created we don’t know which direction the cell cycle is going - it could be forward or backward.) Then there are 10 columns corresponding to 10 different genes.

I’m going to order the rows by cell cycle (theta, first column) as this will make things much easier later.

# order the data
o = order(d[,1])
d = d[o,]
plot(d$theta)

library(genlasso)

Loading required package: MASS

Loading required package: Matrix

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

d2.tf = trendfilter(d[,2],ord = 1)

Warning: 'rBind' is deprecated.
 Since R version 3.2.0, base's rbind() should work fine with S4 objects

d2.tf.cv = cv.trendfilter(d2.tf) # performs 5-fold CV

Fold 1 ... Fold 2 ... Fold 3 ... Fold 4 ... Fold 5 ... 

plot(d[,1],d[,2],xlab="cell cycle",ylab="expression")
lines(d[,1],predict(d2.tf, d2.tf.cv$lambda.min)$fit,col=2,lwd=3)

subset = sort(sample(1:nrow(d),200))
x = d[subset,1]
y = d[subset,2]
x = x/max(x) # normalize to be in 0,1
y.gpfit = GPfit::GP_fit(x,y)
plot(x,y)
lines(x,predict(y.gpfit)$Y_hat,col=2)

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] genlasso_1.3  igraph_1.2.1  Matrix_1.2-14 MASS_7.3-49  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16      knitr_1.20        whisker_0.3-2    
 [4] magrittr_1.5      workflowr_1.0.1   GPfit_1.0-0      
 [7] lattice_0.20-35   stringr_1.3.0     tools_3.3.2      
[10] grid_3.3.2        R.oo_1.22.0       git2r_0.21.0     
[13] htmltools_0.3.6   yaml_2.1.18       rprojroot_1.3-2  
[16] digest_0.6.15     lhs_0.16          R.utils_2.6.0    
[19] evaluate_0.10.1   rmarkdown_1.9     stringi_1.1.7    
[22] backports_1.1.2   R.methodsS3_1.7.1 pkgconfig_2.0.1  

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