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Merge pull request #81 from jasenfinch/devel
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v0.14.4
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jasenfinch authored Nov 8, 2021
2 parents 83c4f9d + 72a56c0 commit 43a68c9
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Package: metabolyseR
Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
Version: 0.14.3
Version: 0.14.4
Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
URL: https://jasenfinch.github.io/metabolyseR
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4 changes: 4 additions & 0 deletions NEWS.md
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# metabolyseR 0.14.4

* Console output from [`imputeAll()`](https://jasenfinch.github.io/metabolyseR/reference/impute.html) now suppressed.

# metabolyseR 0.14.3

* Temporarily added [jasenfinch/missForest](https://github.com/jasenfinch/missForest) as a remote until [stekhoven/missForest](https://github.com/stekhoven/missForest) pull request [#25](https://github.com/stekhoven/missForest/pull/25) is resolved.
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13 changes: 7 additions & 6 deletions R/impute.R
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Expand Up @@ -84,11 +84,11 @@ setMethod('imputeAll',signature = 'AnalysisData',

da[da == 0] <- NA

suppressWarnings({
capture.output({
da <- missForest(da,parallelize = parallel)
})
})
capture.output(
suppressMessages(
da <- missForest(da,parallelize = parallel)
)
)

dat(d_to_impute) <- as_tibble(da$ximp)

Expand Down Expand Up @@ -137,7 +137,8 @@ setMethod('imputeClass',signature = 'AnalysisData',
keepClasses(cls = cls,classes = .x) %>%
imputeAll(occupancy = occupancy,seed = seed,parallel = 'no')
},
.options = furrr_options(seed = seed))
.options = furrr_options(seed = seed,
stdout = FALSE))

d <- d %>%
bindRows() %>%
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1 change: 1 addition & 0 deletions README.Rmd
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Expand Up @@ -20,6 +20,7 @@ knitr::opts_chunk$set(collapse = TRUE,
[![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master)
[![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION)
[![DOI](https://zenodo.org/badge/88983134.svg)](https://zenodo.org/badge/latestdoi/88983134)
[![GitHub release](https://img.shields.io/github/release/jasenfinch/metabolyseR.svg)](https://GitHub.com/jasenfinch/metabolyseR/releases/)
<!-- badges: end -->

> **A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.**
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34 changes: 18 additions & 16 deletions README.md
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Expand Up @@ -11,6 +11,8 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
[![codecov](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metabolyseR/branch/master)
[![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metabolyseR/blob/master/DESCRIPTION)
[![DOI](https://zenodo.org/badge/88983134.svg)](https://zenodo.org/badge/latestdoi/88983134)
[![GitHub
release](https://img.shields.io/github/release/jasenfinch/metabolyseR.svg)](https://GitHub.com/jasenfinch/metabolyseR/releases/)
<!-- badges: end -->

> **A tool kit for pre-treatment, modelling, feature selection and
Expand All @@ -21,9 +23,9 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
This package provides a tool kit of methods for metabolomics analyses
that includes:

- data pre-treatment
- multivariate and univariate modelling/data mining techniques
- correlation analysis
- data pre-treatment
- multivariate and univariate modelling/data mining techniques
- correlation analysis

## Installation

Expand Down Expand Up @@ -168,7 +170,7 @@ anova_results <- d %>%
```

A table of the significantly explanatory features can be extracted with
a bonferroni correction adjusted p value \< 0.05 using:
a bonferroni correction adjusted p value &lt; 0.05 using:

``` r
explan_feat <- explanatoryFeatures(anova_results,threshold = 0.05)
Expand All @@ -177,18 +179,18 @@ explan_feat <- explanatoryFeatures(anova_results,threshold = 0.05)
``` r
explan_feat
#> # A tibble: 379 × 10
#> Response Comparison Feature term df sumsq meansq statistic p.value
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 day 1~2~3~4~5~H N341 response 5 3.88e-4 7.76e-5 137. 1.55e-46
#> 2 day 1~2~3~4~5~H N133 response 5 7.00e-5 1.40e-5 126. 8.63e-45
#> 3 day 1~2~3~4~5~H N163 response 5 6.01e-5 1.20e-5 117. 2.95e-43
#> 4 day 1~2~3~4~5~H N1087 response 5 2.42e-6 4.84e-7 99.8 5.61e-40
#> 5 day 1~2~3~4~5~H N171 response 5 2.25e-7 4.50e-8 95.7 3.84e-39
#> 6 day 1~2~3~4~5~H N513 response 5 3.38e-6 6.76e-7 95.3 4.78e-39
#> 7 day 1~2~3~4~5~H N1025 response 5 2.78e-6 5.56e-7 91.0 3.91e-38
#> 8 day 1~2~3~4~5~H N342 response 5 3.71e-6 7.41e-7 90.3 5.32e-38
#> 9 day 1~2~3~4~5~H N1083 response 5 5.11e-5 1.02e-5 89.0 1.06e-37
#> 10 day 1~2~3~4~5~H N1085 response 5 1.10e-5 2.19e-6 83.4 1.92e-36
#> Response Comparison Feature term df sumsq meansq statistic p.value
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 day 1~2~3~4~5~H N341 respo… 5 3.88e-4 7.76e-5 137. 1.55e-46
#> 2 day 1~2~3~4~5~H N133 respo… 5 7.00e-5 1.40e-5 126. 8.63e-45
#> 3 day 1~2~3~4~5~H N163 respo… 5 6.01e-5 1.20e-5 117. 2.95e-43
#> 4 day 1~2~3~4~5~H N1087 respo… 5 2.42e-6 4.84e-7 99.8 5.61e-40
#> 5 day 1~2~3~4~5~H N171 respo… 5 2.25e-7 4.50e-8 95.7 3.84e-39
#> 6 day 1~2~3~4~5~H N513 respo… 5 3.38e-6 6.76e-7 95.3 4.78e-39
#> 7 day 1~2~3~4~5~H N1025 respo… 5 2.78e-6 5.56e-7 91.0 3.91e-38
#> 8 day 1~2~3~4~5~H N342 respo… 5 3.71e-6 7.41e-7 90.3 5.32e-38
#> 9 day 1~2~3~4~5~H N1083 respo… 5 5.11e-5 1.02e-5 89.0 1.06e-37
#> 10 day 1~2~3~4~5~H N1085 respo… 5 1.10e-5 2.19e-6 83.4 1.92e-36
#> # … with 369 more rows, and 1 more variable: adjusted.p.value <dbl>
```

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