Source file: notebooks/runtimes/indrop_esc.Rmd

Last updated: 2018-05-29

Code version: 5b1d31c

library(ggplot2)
library(ggrastr)
library(ggpubr)
library(dplyr)
library(Matrix)
library(parallel)
library(dropestr)
library(dropEstAnalysis)

theme_set(theme_base)

set.seed(42)
kOutputFolder <- '../../output/'
kDataPath <- '../../data/'
kEstDataPath <- paste0(kDataPath, 'dropest/SRR1784310/runtimes/est_2018_03_15_real/')
holder <- readRDS(paste0(kEstDataPath, 'cell.counts.rds'))

UMI collisions

times_coll <- sapply(1:10, function(i) TimeCollisions(holder))
mean(times_coll, trim=0.2)
[1] 10.247

Error corrections directional

times_directional <- sapply(1:10, function(i) TimeUmiErrors(holder$reads_per_umi_per_cell, 
                                                            'directional', mc.cores=10))
print(times_directional)
elapsed elapsed elapsed elapsed elapsed elapsed elapsed elapsed elapsed 
 73.628  54.244  61.960  63.587  67.917  68.531  66.631  62.464  67.834 
elapsed 
 50.537 
mean(times_directional, trim=0.1)
[1] 64.146

Error corrections Bayesian

times_bayesian <- sapply(1:5, function(i) TimeUmiErrors(holder$reads_per_umi_per_cell, 
                                                        mc.cores=10))
print(times_bayesian)
elapsed elapsed elapsed elapsed elapsed 
870.233 922.000 930.293 879.992 915.920 
mean(times_bayesian, trim=0.1)
[1] 903.6876

Quality scoring

times_quality <- sapply(1:10, function(i) TimeQuality(holder, mit.chromosome.name='chrM'))
print(times_quality)
elapsed elapsed elapsed elapsed elapsed elapsed elapsed elapsed elapsed 
  6.207   5.425   4.457   4.348   4.483   4.277   4.243   4.223   6.521 
elapsed 
  4.473 
mean(times_quality, trim=0.1)
[1] 4.739125

Session information

value
version R version 3.4.1 (2017-06-30)
os Ubuntu 14.04.5 LTS
system x86_64, linux-gnu
ui X11
language (EN)
collate en_US.UTF-8
tz America/New_York
date 2018-05-29
package loadedversion date source
1 assertthat 0.2.0 2017-04-11 CRAN (R 3.4.1)
2 backports 1.1.2 2017-12-13 CRAN (R 3.4.1)
4 bindr 0.1 2016-11-13 CRAN (R 3.4.1)
5 bindrcpp 0.2 2017-06-17 CRAN (R 3.4.1)
6 clisymbols 1.2.0 2017-05-21 CRAN (R 3.4.1)
7 colorspace 1.3-2 2016-12-14 CRAN (R 3.4.1)
10 digest 0.6.15 2018-01-28 cran (@0.6.15)
11 dplyr 0.7.4 2017-09-28 CRAN (R 3.4.1)
12 dropEstAnalysis 0.6.0 2018-05-16 local (VPetukhov/dropEstAnalysis@NA)
13 dropestr 0.7.7 2018-03-17 local (@0.7.7)
14 evaluate 0.10.1 2017-06-24 CRAN (R 3.4.1)
15 ggplot2 2.2.1 2016-12-30 CRAN (R 3.4.1)
16 ggpubr 0.1.6 2017-11-14 CRAN (R 3.4.1)
17 ggrastr 0.1.5 2017-12-28 Github (VPetukhov/ggrastr@cc56b45)
18 git2r 0.21.0 2018-01-04 cran (@0.21.0)
19 glue 1.2.0 2017-10-29 CRAN (R 3.4.1)
23 gtable 0.2.0 2016-02-26 CRAN (R 3.4.1)
24 highr 0.6 2016-05-09 CRAN (R 3.4.1)
25 htmltools 0.3.6 2017-04-28 CRAN (R 3.4.1)
26 KernSmooth 2.23-15 2015-06-29 CRAN (R 3.4.0)
27 knitr 1.20 2018-02-20 cran (@1.20)
28 ks 1.11.0 2018-01-16 local (VPetukhov/ks@NA)
29 lattice 0.20-35 2017-03-25 CRAN (R 3.4.1)
30 lazyeval 0.2.1 2017-10-29 CRAN (R 3.4.1)
31 magrittr 1.5 2014-11-22 CRAN (R 3.4.1)
32 Matrix 1.2-12 2017-11-16 CRAN (R 3.4.1)
33 mclust 5.4 2017-11-22 CRAN (R 3.4.1)
35 munsell 0.4.3 2016-02-13 CRAN (R 3.4.1)
36 mvtnorm 1.0-7 2018-01-26 cran (@1.0-7)
38 pcaPP 1.9-73 2018-01-14 cran (@1.9-73)
39 pkgconfig 2.0.1 2017-03-21 CRAN (R 3.4.1)
40 plyr 1.8.4 2016-06-08 CRAN (R 3.4.1)
41 R6 2.2.2 2017-06-17 CRAN (R 3.4.1)
42 Rcpp 0.12.17 2018-05-18 cran (@0.12.17)
43 rlang 0.1.4 2017-11-05 CRAN (R 3.4.1)
44 rmarkdown 1.9 2018-03-01 CRAN (R 3.4.1)
45 rprojroot 1.3-2 2018-01-03 cran (@1.3-2)
46 scales 0.5.0 2017-08-24 CRAN (R 3.4.1)
47 sessioninfo 1.0.0 2017-06-21 CRAN (R 3.4.1)
49 stringi 1.1.7 2018-03-12 cran (@1.1.7)
50 stringr 1.3.0 2018-02-19 cran (@1.3.0)
51 tibble 1.3.4 2017-08-22 CRAN (R 3.4.1)
54 withr 2.1.2 2018-03-15 cran (@2.1.2)
55 yaml 2.1.18 2018-03-08 cran (@2.1.18)

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