# Sep2015
higher sensitivity:
metaseqr(
    sample.list=file.path(the.path,"targets_run213.txt"),
    contrast=c("TZEROHOURS_vs_TSEVENDAYS"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_0h_vs_7d_run213c"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("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")
)

#

count_type="exon"

# Jul2015
metaseqr(
    sample.list=file.path(the.path,"targets_run213a.txt"),
    contrast=c("TZEROHOURS_vs_TONEHOUR"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_0h_vs_1h_run213"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("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_run213b.txt"),
    contrast=c("TZEROHOURS_vs_TTHREEHOURS"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_0h_vs_3h_run213"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("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_run213c.txt"),
    contrast=c("TZEROHOURS_vs_TSIXHOURS"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_0h_vs_6h_run213"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("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_run213d.txt"),
    contrast=c("TZEROHOURS_vs_TTWENTYFOURHOURS"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_0h_vs_24h_run213"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("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_run213e.txt"),
    contrast=c("TZEROHOURS_vs_TSEVENDAYS"),
    org="mm9",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_0h_vs_7d_run213"),
    qc.plots=c(
        "mds","biodetection","countsbio","saturation","readnoise",
        "correl","pairwise","boxplot","volcano","biodist","deheatmap"
    ),
    pcut=0.05,
    export.what=c("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")
)