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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a gene expresssion matrix with Ensembl gene ids (rows correspond to genes)
the gene biotype like "lincRNA" or a vector of querie(s) - one or multiple genes ids
remove 30 percent of the variance in the data by PCA
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.
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")
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# 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)
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