Working with lfproQC package"

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

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

options(rmarkdown.html_vignette.check_title = FALSE)

To attach the package in R studio

library(lfproQC)

To find the best combination of normalization and imputation method for the dataset

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

PCV values result

yeast$`PCV Result`

PEV values result

yeast$`PEV Result`

PMAD values result

yeast$`PMAD Result`

Best combinations

yeast$`Best combinations`

To visualize the normality by different exploratory plots

1. By boxplot

Boxplot_data(yeast$`rlr_knn_data`)  

2. By density plot

Densityplot_data(yeast$`rlr_knn_data`)

3. By correlation heatmap

Corrplot_data(yeast$`rlr_knn_data`)

4. By MDS plot

MDSplot_data(yeast$`rlr_knn_data`)

5. By QQ-plot

QQplot_data(yeast$`rlr_knn_data`)

Differential expression analysis

To Calculate the top-table values

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

To visualize the different kinds of differentially abundant proteins, such as up-regulated, down-regulated, significant and non-significant proteins

By MA plot

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

By volcano plot

de_yeast_volcano <- volcanoplot_DE_fn (top_table_yeast,-1,1,0.05)
de_yeast_volcano$`Volcano Plot`

Both of the above plots give same result.

To obtain the overall differentially abundant proteins result

de_yeast_MA$`Result `

To find the up-regulated proteins

de_yeast_MA$`Up-regulated`

To find the down-regulated proteins

de_yeast_MA$`Down-regulated`

To find the other significant proteins

de_yeast_MA$`Significant`

To find the non-significant proteins

de_yeast_MA$`Non-significant`

The overall workflow of working with the 'lfproQC' package

library(knitr)

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

Session Information

sessionInfo()

lfproQC documentation built on Oct. 10, 2024, 5:06 p.m.