lnc_gsea: lncRNA associated Gene Set Enrichment Analysis
In ylab-hi/lncGSEA: lncRNA Associated Gene Set Enrichement Analysis

TCGA samples are either stratified by lncRNA's expression and then calculate log2FC of high vs low expressed groups for each genes, or calculate correlation coefficient between each gene's expression and the lncRNA's expression. Genes are then ordered by logFC or correlation coefficent in a descending order. The ranked gene list will be used by 'fgsea' for pre-ranked GSEA.

lnc_gsea(
  tid_cohort,
  metric = c("cor", "logFC"),
  cor.method = c("pearson", "spearman"),
  genelist = FALSE,
  geneset = NULL,
  pathway = NULL
)

`tid_cohort`	A output of data frame from pre_gsea function
`metric`	A string of character, showing which metric is used for rank
`cor.method`	"pearson" or "spearman" method for cor metric
`genelist`	TRUE or FALSE for output ordered gene list or not
`geneset`	A string of character, showing the path where gmt is
`pathway`	A string of character, showing one of pathway in the gmt file

A file with the GSEA results.If pathway is provided, its enrichment plot will be produced too. If genelist is TRUE, also get a file for a ranked gene list with ranking metrics, which can be used for GSEA desktop app provided by Broad Institute.

ylab-hi/lncGSEA documentation built on Aug. 20, 2020, 9:41 a.m.