/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("ABFF_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABFF_vs_cagAKO"),
    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.txt"),
    contrast=c("ABCC_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCC_vs_AGS"),
    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.txt"),
    contrast=c("ABCCC_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCCC_vs_AGS"),
    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.txt"),
    contrast=c("ABFF_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABFF_vs_AGS"),
    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.txt"),
    contrast=c("ABFFF_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABFFF_vs_AGS"),
    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.txt"),
    contrast=c("cagAKO_vs_AGS"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_cagAKO_vs_AGS"),
    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.txt"),
    contrast=c("ABCC_vs_ABCCC"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCC_vs_ABCCC"),
    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.txt"),
    contrast=c("ABCC_vs_ABFF"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCC_vs_ABFF"),
    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.txt"),
    contrast=c("ABFF_vs_ABFFF"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABFF_vs_ABFFF"),
    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.txt"),
    contrast=c("ABCC_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCC_vs_cagAKO"),
    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.txt"),
    contrast=c("ABCCC_vs_ABFFF"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCCC_vs_ABFFF"),
    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.txt"),
    contrast=c("ABCCC_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCCC_vs_cagAKO"),
    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.txt"),
    contrast=c("ABFFF_vs_cagAKO"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABFFF_vs_cagAKO"),
    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.txt"),
    contrast=c("ABCC_vs_ABCCC"),
    org="hg19",
    refdb="refseq",
    normalization="edger",
    statistics="edger",
    export.where=file.path(the.path,"metaseqr_ABCC_vs_ABCCC"),
    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")
)

#@
chromosome	start	end	gene_id	gc_content	strand	gene_name	biotype	p-value_edger	FDR_edger	log2_normalized_fold_change_ABCC_vs_cagAKO	log2_normalized_mean_counts_ABCC	log2_normalized_median_counts_ABCC	log2_normalized_sd_counts_ABCC	log2_normalized_mad_counts_ABCC	log2_normalized_cv_counts_ABCC	log2_normalized_rcv_counts_ABCC	log2_normalized_mean_counts_cagAKO	log2_normalized_median_counts_cagAKO	log2_normalized_sd_counts_cagAKO	log2_normalized_mad_counts_cagAKO	log2_normalized_cv_counts_cagAKO	log2_normalized_rcv_counts_cagAKO	log2_normalized_counts_ABCC1	log2_normalized_counts_ABCC2	log2_normalized_counts_cagAKO1	log2_normalized_counts_cagAKO2	LN	AR	MD	MN	QN	KN	CM	BT
chr11	102641232	102651359	NM_002425	0.3611	-	MMP10	protein_coding	NA	NA	-1.4594316186373	5.52082957581861	5.52082957581861	0.801340448865309	0.840090479329086	0.145148557451439	0.152167435671028	4.14960400919364	4.14960400919364	0.343248601261948	0.3598469069813	0.0827183992741151	0.0867183726890669	6.08746284125034	4.95419631038687	4.39231742277876	3.90689059560852	0	0	1	0	0	0	0	0
chr11	102447565	102496063	NM_004771	0.3965	-	MMP20	protein_coding	NA	NA	-1.96219796728762	6.76745538406266	6.76745538406266	0.554959962422148	0.581795891496345	0.08200422920099	0.0859696678409543	4.84412515456659	4.84412515456659	0.283223086131075	0.296918767200418	0.0584673345741446	0.0612946110445786	6.37503943134692	7.15987133677839	4.64385618977472	5.04439411935845	0	0	1	0	0	0	0	0