justlinc-methods {LINC} | R Documentation

## Co-Expression Analysis Of ncRNA Genes In One Step

### Description

`justlinc` is a wrapper that uses different functions of the LINC package. It applies fixed thresholds for gene selection and requires only an (unprocessed) expression matrix as input. This enables a fast co-expression analysis with or without a list candidates.

### Usage

    justlinc(object,
        targetGenes = "lincRNA",
               rmPC = TRUE)

### Arguments

`object` | a gene expresssion matrix with Ensembl gene ids (rows correspond to genes)
`targetGenes` | the gene biotype like "lincRNA" or a vector of querie(s) - one or multiple genes ids
`rmPC` | remove 30 percent of the variance in the data by PCA `TRUE` or not `FALSE`.

### Details

This function was built for expression matrices which uses the Ensembl gene system with gene expression values for over 50.000 genes. The input will be matched with a static gene annotation. Genes will be selected for median expression and variance. The final correlation matrix of protein-coding genes versus the target genes (lincRNAs) considers 5000 protein-coding genes and 500 target genes. Enriched pathways will be computed for the co-expressed genes showing the highest Spearman's rank correlation. In case `targetGenes = "lincRNA"`, then the function will search for the 10 best lincRNAs. Supplying a vector of gene ids the method will determine the best co-expressed genes for the given queries. Importanly, this function is only a wrapper. Thresholds can be changed using `linc` and related functions.

### Value

depending on the input in `targetGenes` one or two plots and the result of the co-expression analysis

### Methods

`signature(object = "matrix")`

  (see details)

### Author(s)

Manuel Goepferich

### See Also

`linc`

### Examples

    # NOT RUN:

    # large gene expression matrix not avaiable in this version

    # data(LIVER_EXPR)
    # a gene expression matrix with > 50,000 genes
    # str(GTEX_LIVER_CRUDE)

    # 'justlinc' will search for the 10 best candidates
    try(justlinc(GTEX_LIVER_CRUDE), silent = TRUE)

    # 'justlinc' called with queries
    my_lincRNAs <- c("ENSG00000224153", "ENSG00000197813",
                     "ENSG00000179136", "ENSG00000259439",
                     "ENSG00000267462")

    try(justlinc(GTEX_LIVER_CRUDE, targetGenes = my_lincRNAs), silent = TRUE)

[Package LINC version 1.14.0 Index]