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adomingues/deseq2_factors.R

Created December 3, 2018 12:20
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BioC question re factor levels after collapseReplicates
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deseq2_factors.R
samples <- structure(list(sample = structure(c(3L, 4L, 5L, 6L, 7L, 8L, 9L,
10L, 1L, 2L, 14L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 20L, 21L,
22L, 23L, 23L, 24L, 25L, 11L, 12L, 13L), .Label = c("wt_Fish_10dpf_rep1_mRNA",
"wt_Fish_10dpf_rep2_mRNA", "wt_Fish_1dpf_rep1_mRNA", "wt_Fish_1dpf_rep2_mRNA",
"wt_Fish_2dpf_rep1_mRNA", "wt_Fish_2dpf_rep2_mRNA", "wt_Fish_3dpf_rep1_mRNA",
"wt_Fish_3dpf_rep2_mRNA", "wt_Fish_6dpf_rep1_mRNA", "wt_Fish_6dpf_rep2_mRNA",
"wt_PGCs_10dpf_rep1_mRNA", "wt_PGCs_10dpf_rep2_mRNA", "wt_PGCs_10dpf_rep3_mRNA",
"wt_PGCs_1dpf_rep1_mRNA", "wt_PGCs_1dpf_rep2_mRNA", "wt_PGCs_1dpf_rep3_mRNA",
"wt_PGCs_2dpf_rep1_mRNA", "wt_PGCs_2dpf_rep2_mRNA", "wt_PGCs_2dpf_rep3_mRNA",
"wt_PGCs_3dpf_rep1_mRNA", "wt_PGCs_3dpf_rep2_mRNA", "wt_PGCs_3dpf_rep3_mRNA",
"wt_PGCs_6dpf_rep1_mRNA", "wt_PGCs_6dpf_rep2_mRNA", "wt_PGCs_6dpf_rep3_mRNA",
"wt_zygotes_0hpf_rep1_mRNA", "wt_zygotes_0hpf_rep2_mRNA", "wt_zygotes_0hpf_rep3_mRNA"
), class = "factor"), DevStage = structure(c(2L, 2L, 3L, 3L,
4L, 4L, 5L, 5L, 6L, 6L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L,
4L, 5L, 5L, 5L, 5L, 6L, 6L, 6L), .Label = c("0hpf", "1dpf", "2dpf",
"3dpf", "6dpf", "10dpf"), class = "factor"), Type = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L,
1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L), .Label = c("paired",
"single"), class = "factor"), Treatment = c("control", "control",
"control", "control", "control", "control", "control", "control",
"control", "control", "treated", "treated", "treated", "treated",
"treated", "treated", "treated", "treated", "treated", "treated",
"treated", "treated", "treated", "treated", "treated", "treated",
"treated", "treated")), row.names = c("wt_Fish_1dpf_rep1_mRNA.paired",
"wt_Fish_1dpf_rep2_mRNA.paired", "wt_Fish_2dpf_rep1_mRNA.paired",
"wt_Fish_2dpf_rep2_mRNA.paired", "wt_Fish_3dpf_rep1_mRNA.paired",
"wt_Fish_3dpf_rep2_mRNA.paired", "wt_Fish_6dpf_rep1_mRNA.paired",
"wt_Fish_6dpf_rep2_mRNA.paired", "wt_Fish_10dpf_rep1_mRNA.paired",
"wt_Fish_10dpf_rep2_mRNA.paired", "wt_PGCs_1dpf_rep1_mRNA.paired",
"wt_PGCs_1dpf_rep1_mRNA.single", "wt_PGCs_1dpf_rep2_mRNA.paired",
"wt_PGCs_1dpf_rep3_mRNA.paired", "wt_PGCs_2dpf_rep1_mRNA.paired",
"wt_PGCs_2dpf_rep2_mRNA.paired", "wt_PGCs_2dpf_rep3_mRNA.paired",
"wt_PGCs_3dpf_rep1_mRNA.paired", "wt_PGCs_3dpf_rep1_mRNA.single",
"wt_PGCs_3dpf_rep2_mRNA.paired", "wt_PGCs_3dpf_rep3_mRNA.paired",
"wt_PGCs_6dpf_rep1_mRNA.paired", "wt_PGCs_6dpf_rep1_mRNA.single",
"wt_PGCs_6dpf_rep2_mRNA.paired", "wt_PGCs_6dpf_rep3_mRNA.paired",
"wt_PGCs_10dpf_rep1_mRNA.paired", "wt_PGCs_10dpf_rep2_mRNA.paired",
"wt_PGCs_10dpf_rep3_mRNA.paired"), class = "data.frame")
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