# the exomePeak R-package has two main functions:
# 1. peak detection
# 2. comparison of two conditions
# please feel free to contact jia.meng@hotmail.com for any questions
# specify the parameters
GENE_ANNO_GTF=system.file("extdata", "example.gtf", package="exomePeak")
f1=system.file("extdata", "IP1.bam", package="exomePeak")
f2=system.file("extdata", "IP2.bam", package="exomePeak")
f3=system.file("extdata", "IP3.bam", package="exomePeak")
f4=system.file("extdata", "IP4.bam", package="exomePeak")
IP_BAM=c(f1,f2,f3,f4)
f1=system.file("extdata", "Input1.bam", package="exomePeak")
f2=system.file("extdata", "Input2.bam", package="exomePeak")
f3=system.file("extdata", "Input3.bam", package="exomePeak")
INPUT_BAM=c(f1,f2,f3)
f1=system.file("extdata", "treated_IP1.bam", package="exomePeak")
TREATED_IP_BAM=c(f1)
f1=system.file("extdata", "treated_Input1.bam", package="exomePeak")
TREATED_INPUT_BAM=c(f1)
# peak calling and comparison of two conditions
result = exomepeak(GENE_ANNO_GTF=GENE_ANNO_GTF, IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM,
TREATED_IP_BAM=TREATED_IP_BAM, TREATED_INPUT_BAM=TREATED_INPUT_BAM)
# or peak calling only, using data from only one condition with the following script
# result = exomepeak(GENE_ANNO_GTF=GENE_ANNO_GTF, IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM)
# alternatively, the gene annotation can be downloaded directly from internet with GENOME (and UCSC_TABLE_NAME).
# this will take a long time with the entire transcriptome of hg19
# result = exomepeak(GENOME="hg19", IP_BAM=IP_BAM, INPUT_BAM=INPUT_BAM)
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