TCGA lncRNA的提取

gdcRNAtools是按照大类来分的，返回的对象那个里面的lncRNA就是lncRNA
，一般的lncRNA我们可以按照gene_biotype 分为下面这些，进行提取就行了

3prime_overlapping_ncRNA
antisense_RNA
bidirectional_promoter_lncRNA
lincRNA
macro_lncRNA
non_coding
processed_transcript
sense_intronic
sense_overlapping

gdcRNAtools找差异

DEGAll <- gdcDEAnalysis(counts     = new_expMatrix, 
                        group      = metaMatrix.RNA$sample_type, 
                        comparison = 'PrimaryTumor-SolidTissueNormal', 
                        method     = 'edgeR',
                        n.cores = 7)

table(DEGAll$group)

image.png

因为中间有过滤参数，才会出现56830变为15319

image.png