Perform PCA on RNAseq data from one tumor type and its matched healthy tissue

Source: R/PCA.R

A composite function performs PCA on RNAseq data from one tumor type and its matched healthy tissue, and plot results

.plot_PCA_TCGA_GTEX_tumor(gene_list, sample_type)

Arguments

gene_list

gene names in a vector of characters

sample_type

tissue type

Details

This function

  • selects RNAseq data of gene_list genes in TCGA tumors and GTEx healthy tissues with the same tissue of origin from TCGA_GTEX_RNAseq_sampletype, by .get_df_subset().

  • performs PCA on combined tumor and healthy samples by .RNAseq_PCA(),

  • plots results as biplot, scree and matrix plots by .biplot()

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()

Examples

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