library ( DESeq2 )
library ( ggplot2 )
library ( clusterProfiler )
library ( biomaRt )
library ( ReactomePA )
library ( DOSE )
library ( KEGG.db )
library ( org.Hs.eg.db )
library ( pheatmap )
library ( genefilter )
library ( RColorBrewer )
library ( GO.db )
library ( topGO )
library ( dplyr )
library ( gage )
library ( ggsci )
bamfilesSE <- list.files ( path = "bamfile_SE" ,
pattern = "*.bam$" ,
full.names = TRUE )
bamfilesPE <- list.files ( path = "bamfile_PE" ,
pattern = "*.bam$" ,
full.names = TRUE )
bamfilesSE
conteo <- featureCounts ( files = bamfilesSE ,
annot.ext = "GCF_000001735.4_TAIR10.1_genomic.gff" ,
isGTFAnnotation = TRUE ,
GTF.featureType = "gene" ,
GTF.attrType = "ID" ,
isPairedEnd = FALSE ,
requireBothEndsMapped = FALSE ,
minMQS = 20 ,
strandSpecific = 2 )
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.6.4
//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 10 BAM files ||
|| ||
|| SRR390302_sortedByCoord.out.bam ||
|| SRR390303_sortedByCoord.out.bam ||
|| SRR390304_sortedByCoord.out.bam ||
|| SRR390306_sortedByCoord.out.bam ||
|| SRR390307_sortedByCoord.out.bam ||
|| SRR390308_sortedByCoord.out.bam ||
|| SRR390309_sortedByCoord.out.bam ||
|| SRR390311_sortedByCoord.out.bam ||
|| SRR390312_sortedByCoord.out.bam ||
|| SRR390313_sortedByCoord.out.bam ||
|| ||
|| Paired-end : no ||
|| Count read pairs : no ||
|| Annotation : GCF_000001735.4_TAIR10.1_genomic.gff (GTF) ||
|| Dir for temp files : . ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| Min overlapping bases : 1 ||
|| ||
\\============================================================================//
conteo $ counts
write.table ( conteo $ counts , file = "rawSE_counts.txt" , sep = "\t" )
data <- read.table ( "rawSE_counts.txt" , header = TRUE , row.names = 1 )
head ( data )
colnames ( data ) <- gsub ( "_sortedByCoord.out.bam" , "" , colnames ( data ), fixed = T )
colnames ( data ) <- gsub ( ".." , "" , colnames ( data ), fixed = T )
row.names ( data ) <- gsub ( "gene-" , "" , rownames ( data ), fixed = T )
head ( data )
metadata <- read.delim ( "muestras.txt" , row.names = 1 )
metadata $ sampleid <- row.names ( metadata )
metadata <- metadata [ match ( colnames ( data ), metadata $ sampleid ),]
metadata
ddsMat <- DESeqDataSetFromMatrix ( countData = data ,
colData = metadata ,
design = ~ Group )
ddsMat <- DESeq ( ddsMat )
# Get results from testing with FDR adjust pvalues
results <- results ( ddsMat , pAdjustMethod = "fdr" , alpha = 0.05 )
# Generate summary of testing.
summary ( results )
mcols ( results , use.names = T )
results