/home/moulos/Rbase/bin/R

library(metaseqR)
the.path="/data/images/proton/run272/www"
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCC_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCC_vs_cagAKO"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABFF_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABFF_vs_cagAKO"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)




metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCC_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCC_vs_AGS"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCCC_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCCC_vs_AGS"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABFF_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABFF_vs_AGS"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABFFF_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABFFF_vs_AGS"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("cagAKO_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_cagAKO_vs_AGS"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

#@
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCC_vs_ABCCC"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCC_vs_ABCCC"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCC_vs_ABFF"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCC_vs_ABFF"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABFF_vs_ABFFF"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABFF_vs_ABFFF"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)



#@
metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCCC_vs_ABFFF"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCCC_vs_ABFFF"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCCC_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCCC_vs_cagAKO"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)

metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABFFF_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABFFF_vs_cagAKO"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)


metaseqr(
    sample.list=file.path(the.path,"targets.txt"),
    contrast=c("ABCC_vs_ABCCC"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr2_ABCC_vs_ABCCC"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,    gene.filters=NULL,
    exon.filters=NULL,
    export.what=c("flags","annotation","p.value","adj.p.value","fold.change","stats",
        "counts"),
    export.scale=c("log2"),
    export.values="normalized",
    export.counts.table=TRUE,
    restrict.cores=0.3,
fig.format=c("png","pdf")
)