justlinc-methods: Co-Expression Analysis Of ncRNA Genes In One Step
In ManuelGoepferich/LINC: co-expression of lincRNAs and protein-coding genes

Description Usage Arguments Details Value Methods Author(s) See Also Examples

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.

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

`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`.

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.

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

signature(object = "matrix"): (see details)

Manuel Goepferich

linc

# 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)