SPR Workflow Technical Report

Package

systemPipeR 2.3.4

1 load_library

Time: Jun032022_1507s52

1.1 Code:

library(systemPipeR)

1.2 Stdout:

 [1] "systemPipeR"          "ShortRead"            "GenomicAlignments"    "SummarizedExperiment" "Biobase"             
 [6] "MatrixGenerics"       "matrixStats"          "BiocParallel"         "Rsamtools"            "Biostrings"          
[11] "XVector"              "GenomicRanges"        "GenomeInfoDb"         "IRanges"              "S4Vectors"           
[16] "stats4"               "BiocGenerics"         "stats"                "graphics"             "grDevices"           
[21] "utils"                "datasets"             "methods"              "base"                

2 export_iris

Time: Jun032022_1507s52

2.1 Code:

mapply(function(x, y) write.csv(x, y), split(iris, factor(iris$Species)), file.path("results", paste0(names(split(iris, factor(iris$Species))), ".csv")))

2.2 Stdout:

$setosa
NULL

$versicolor
NULL

$virginica
NULL

3 gzip

3.1 SE

Time: Jun032022_1507s52

3.1.1 Code:

gzip -c  results/setosa.csv > results/SE.csv.gz

3.1.2 Stdout:

3.2 VE

Time: Jun032022_1507s52

3.2.1 Code:

gzip -c  results/versicolor.csv > results/VE.csv.gz

3.2.2 Stdout:

3.3 VI

Time: Jun032022_1507s52

3.3.1 Code:

gzip -c  results/virginica.csv > results/VI.csv.gz

3.3.2 Stdout:

4 gunzip

4.1 SE

Time: Jun032022_1507s52

4.1.1 Code:

gunzip -c  ./results/gzip/SE.csv.gz > results/SE.csv

4.1.2 Stdout:

4.2 VE

Time: Jun032022_1507s52

4.2.1 Code:

gunzip -c  ./results/gzip/VE.csv.gz > results/VE.csv

4.2.2 Stdout:

4.3 VI

Time: Jun032022_1507s52

4.3.1 Code:

gunzip -c  ./results/gzip/VI.csv.gz > results/VI.csv

4.3.2 Stdout:

5 stats

Time: Jun032022_1507s52

5.1 Code:

df <- lapply(getColumn(sal, step = "gunzip", "outfiles"), function(x) read.delim(x, sep = ",")[-1])
df <- do.call(rbind, df)
stats <- data.frame(cbind(mean = apply(df[, 1:4], 2, mean), sd = apply(df[, 1:4], 2, sd)))
stats$species <- rownames(stats)
plot <- ggplot2::ggplot(stats, ggplot2::aes(x = species, y = mean, fill = species)) + ggplot2::geom_bar(stat = "identity", color = "black", position = ggplot2::position_dodge()) + ggplot2::geom_errorbar(ggplot2::aes(ymin = mean - sd, ymax = mean + sd), width = 0.2, position = ggplot2::position_dodge(0.9))

5.2 Stdout: