inst/doc/user_guide.R

In lfproQC: Quality Control for Label-Free Proteomics Expression Data

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knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

options(rmarkdown.html_vignette.check_title = FALSE)

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library(lfproQC)

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yeast <- best_combination(yeast_data, yeast_groups, data_type = "Protein")

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yeast$`PCV Result`

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yeast$`PEV Result`

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yeast$`PMAD Result`

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yeast$`Best combinations`

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Boxplot_data(yeast$`rlr_knn_data`)  

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Densityplot_data(yeast$`rlr_knn_data`)

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Corrplot_data(yeast$`rlr_knn_data`)

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MDSplot_data(yeast$`rlr_knn_data`)

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QQplot_data(yeast$`rlr_knn_data`)

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top_table_yeast <- top_table_fn(yeast$`rlr_knn_data`, yeast_groups, 2, 1)

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de_yeast_MA <- MAplot_DE_fn(top_table_yeast,-1,1,0.05)
de_yeast_MA$`MA Plot`

## ----echo=TRUE, fig.show='hide', results='hide', warning=FALSE, message=FALSE----
de_yeast_volcano <- volcanoplot_DE_fn (top_table_yeast,-1,1,0.05)
de_yeast_volcano$`Volcano Plot`

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de_yeast_MA$`Result `

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de_yeast_MA$`Up-regulated`

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de_yeast_MA$`Down-regulated`

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de_yeast_MA$`Significant`

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de_yeast_MA$`Non-significant`

## ----setup, include=FALSE-----------------------------------------------------
library(knitr)

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knitr::include_graphics("images/flow1.png", dpi = 72)

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sessionInfo()