pre_gsea: Process expression data for lnc_GSEA function
In ylab-hi/lncGSEA: lncRNA Associated Gene Set Enrichement Analysis

Description Usage Arguments Details Value

Match lncRNA and genes expression (FPKM) for TCGA tumor samples. The first column of the output stores patient ids of a specific tumor cohort from TCGA, the column name is the cohort's name. The second column is the expression of a transcript of the lncRNA you input, the other columns are other genes expression.

1	pre_gsea(cohort, t_id, pathtofile, fortest = FALSE)

`cohort`	A character string which is the short name for cohorts in TCGA
`t_id`	A character string of transcript id, e.g., "T136792", "ENST00000561519"
`pathtofile`	A character string, the path to the datasets downloaded
`fortest`	TRUE or FALSE, default is FALSE. Only for test example

cohort should be one of studies in TCGA, for example, "PRAD" can be used as the function's input to stand for prostate cancer; t_id can be from mitranscriptome database or reflnc database.

A data frame of lncRNA's transcript and other genes' expression in an interested cohort

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