justlinc-methods: Co-Expression Analysis Of ncRNA Genes In One Step

In ManuelGoepferich/LINC_before_DEVEL: annotation of noncoding RNAs and coexpressed genes

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)

ManuelGoepferich/LINC_before_DEVEL documentation built on May 7, 2019, 2:46 p.m.