Perform PCA on RNAseq data from all tumors and healthy tissues

Source: R/PCA.R

A composite function call PCA on RNAseq data from all tumors and healthy tissues and plot results

.plot_PCA_TCGA_GTEX(gene_list)

Arguments

gene_list

gene names in a vector of characters

Details

This function

  • selects RNAseq data of gene_list genes of specific sample types from TCGA_GTEX_RNAseq_sampletype by .get_df_subset().

  • performs three PCAs by .RNAseq_PCA() on

    1. tumor samples from all TCGA cancer types

    2. healthy tissue samples from all GTEx healthy tissue types

    3. TCGA tumors and GTEx healthy tissue samples combined

  • generates biplot, screen plot and matrix plots by .biplot()

  • generates subset biplots for PCA results of combined TCGA tumors and GTEx healthy tissues with .selected_biplot() function

This function is not accessible to the user and will not show at the users' workspace. It can only be called by the exported EIF4F_PCA() function.

Side effects:

(1) PCA biplots (PCA score plot + loading plot) on screen and as pdf files: PCA score plot shows the clusters of samples based on their similarity and loading plot shows how strongly each characteristic influences a principal component.

(2) matrix plots on screen and as pdf files to show the quality of representation of the variables.

(3) scree plots on screen and as pdf files to display how much variation each principal component captures from the data.

See also

Other composite function to call PCA and plot results: .plot_PCA_CPTAC_LUAD(), .plot_PCA_TCGA_GTEX_tumor()

Examples

if (FALSE) {
.plot_PCA_TCGA_GTEX(c(
  "EIF4E", "EIF4G1", "EIF4A1",
  "EIF4EBP1", "PABPC1", "MKNK1", "MKNK2"
))
}