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work_evaluation-etc_variables_pairwise-groupwise.TODOs-scraps-etc.txt
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work_evaluation-etc_rough-draft_Rrp6-WT_SS_timecourse_groupwise.Rmd #MADE #PREP #PCA-ETC
work_evaluation-etc_rough-draft_Rrp6-WT_SS_timecourse_pairwise.Rmd #MADE
work_evaluation-etc_rough-draft_Rrp6-WT_N_G1_pairwise.Rmd #MADE #PREP
work_evaluation-etc_rough-draft_Rrp6-Rtr1-WT_N_Q_groupwise.Rmd #MADE #PREP
work_evaluation-etc_rough-draft_Rrp6-Rtr1-WT_N_Q_pairwise.Rmd #MADE #PREP
work_evaluation-etc_rough-draft_Rrp6-Rtr1-WT_SS_Q_groupwise.Rmd #MADE #PREP #PCA-ETC #INPAIRWISE
work_evaluation-etc_rough-draft_Rrp6-Rtr1-WT_SS_Q_pairwise.Rmd #MADE #PREP #DESEQ2MAVOLCANOETC #NEEDPAIRWISEPCA
# --------------------------------------------------------
Q_SS_wt_r1_r6 <- c(
"WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1",
"WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1",
"r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1",
"r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1",
"r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1",
"r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech2",
"r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1"
)
Q_SS_wt_r6 <- c(
"WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1",
"WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1",
"r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1",
"r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech2",
"r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1"
)
#TODOs ------------------------------------------------------------------------
#TODO Antisense counts matrices in addition to sense counts matrices
#TODO Additional pairwise combinations of samples
#TODO feature_init instead of feature for rownames (etc.); this should sidestep problems with unique names... but #WHERE?
#TODO {6,7,8}a Some kind of column name thing is happening #FIXME
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
New names:
• `value` -> `value...1`
• `value` -> `value...2`
#TODO Do something about this message from DESeq2:
Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error]
#TODO The tibble filtering performed by AG
#TODO Function-ize the generation of MA and volcano plots
#TODO Column subsetting changes based on total number of samples (especially the PCA code)
#DONE title and subtitle
#DONE In the {6,7,8}c code snippets, update the name parameters to select the last term in the GLMs!
#DONE {6,7,8]{d,e} Names of datasets for
#DONE Get rid of all the #TBDs
#TODO Relevant variables res_gw analyses
- Q_N_wt_r1_r6 #INPROGRESS
- strain: r1-n, r6-n, WT
- Q_SS_wt_r1_r6 #INPROGRESS
- strain: r1-n, r6-n, WT
- technical: tech1, tech2
- Q_SS_wt_ot_r1_r6_n3 #INPROGRESS
- strain
- technical
- Q_N_wt_ot_r1_r6_n3 #INPROGRESS
- strain
- tc_SS_wt_r6
- strain: WT, r6-n
- state: DSm2, DSp2, DSp24, DSp48
- technical: tech1, tech2
- tc_SS_wt_t4_r6
- strain: WT, t4-n, r6-n
- state: DSm2, DSp2, DSp24, DSp48
- technical: tech1, tech2
- Q_tc_SS_wt_ot_r1_r6_n3
- strain: WT, o-d, r6-n, n3-d
- state: Q, DSm2, DSp2, DSp24, DSp48
- technical
- G1_Q_SS_N_wt
- state: G1, Q
- transcription: SS, N
# Q SS: WT vs rrp6∆ – Sense
WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech2
r6-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
# G1 SS: WT vs rrp6∆ – Sense
WT_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1
WT_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1
r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep1_tech1
r6-n_G1_day1_tcn_SS_aux-F_tc-F_rep2_tech1
# Q N: WT vs rrp6∆ – Sense
WT_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
WT_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
r6-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
r6-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
# DS –2 SS: WT vs rrp6∆ – Sense
WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
WT_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
r6-n_DSm2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
# DS +2 SS: WT vs rrp6∆ – Sense
WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
WT_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep1_tech1
r6-n_DSp2_day2_tcn_SS_aux-F_tc-T_rep2_tech1
# DS +24 SS: WT vs rrp6∆ – Sense
WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1
WT_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1
r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep1_tech1
r6-n_DSp24_day3_tcn_SS_aux-F_tc-T_rep2_tech1
# DS +48 SS: WT vs rrp6∆ – Sense
WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1
WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech2
WT_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1
r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep1_tech1
r6-n_DSp48_day4_tcn_SS_aux-F_tc-T_rep2_tech1
# Q N: Parent vs NNS depleted – Sense
o-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1
o-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1
n3-d_Q_day7_tcn_N_aux-T_tc-F_rep1_tech1
n3-d_Q_day7_tcn_N_aux-T_tc-F_rep2_tech1
n3-d_Q_day7_tcn_N_aux-T_tc-F_rep3_tech1
# Q SS: Parent vs NNS depleted – Sense
o-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1
o-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1
n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep1_tech1
n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep2_tech1
n3-d_Q_day7_tcn_SS_aux-T_tc-F_rep3_tech1
# Q SS: WT vs rrp6∆ – Antisense
# G1 SS: WT vs rrp6∆ – Antisense
# Q N: WT vs rrp6∆ – Antisense
# DS –2 SS: WT vs rrp6∆ – Antisense
# DS +2 SS: WT vs rrp6∆ – Antisense
# DS +24 SS: WT vs rrp6∆ – Antisense
# DS +48 SS: WT vs rrp6∆ – Antisense
# Q N: Parent vs NNS depleted – Antisense
# Q SS: Parent vs NNS depleted – Antisense
#TRINITY-ETC
#MAYBE
# Q N: WT vs rtr1∆ – Sense
WT_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
WT_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
r1-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
r1-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
# Q SS: WT vs rtr1∆ – Sense
WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
# Q N: rtr1∆ vs rrp6∆ – Sense
r1-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
r1-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
r6-n_Q_day8_tcn_N_aux-F_tc-F_rep1_tech1
r6-n_Q_day8_tcn_N_aux-F_tc-F_rep2_tech1
# Q SS: rtr1∆ vs rrp6∆ – Sense
WT_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
WT_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep1_tech1
r1-n_Q_day8_tcn_SS_aux-F_tc-F_rep2_tech1
#FUN
#TEST-ONLY
WT_Q_day7_tcn_N_aux-F_tc-F_rep2_tech1
WT_Q_day7_tcn_SS_aux-F_tc-F_rep2_tech1