I did my transcripts count using Htseq and now I am trying to use DESeq2 package in R to see differential expression of genes around samples.In order to make the input table for Deseq2 I am using following line of codes:
directory <- C:/Users/hp/Desktop/RNA.seq.data sampleFiles <- c('count.1','count.2','count.3','count.4','count.6','count.7','count.8') sampleCondition<- c('R1control','R1time1','R1time2','R1time4','R2control','R2time1','R2time2','R2time4') sampleTable<- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = sampleCondition) ddsHTSeq<- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition) ddsHTSeq
In the first line of code where I specify path to directory containing count files I always get syntax error. I tried everything like setting working directory and specifying path all that but this is not working. The R version I am using is 3.4.2.