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'))
times_coll <- sapply(1:10, function(i) TimeCollisions(holder))
mean(times_coll, trim=0.2)
[1] 10.247
times_directional <- sapply(1:10, function(i) TimeUmiErrors(holder$reads_per_umi_per_cell,
'directional', mc.cores=10))
print(times_directional)
elapsed elapsed elapsed elapsed elapsed elapsed elapsed elapsed elapsed
73.628 54.244 61.960 63.587 67.917 68.531 66.631 62.464 67.834
elapsed
50.537
mean(times_directional, trim=0.1)
[1] 64.146
times_bayesian <- sapply(1:5, function(i) TimeUmiErrors(holder$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
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
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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