PBTA Histologies: Independent sample base (2 of N)

analyses/independent-samples/00-repeated-samples.Rmd

@@ -4,6 +4,11 @@ output:
   html_notebook:
     toc: true
     toc_float: true
+params:
+  base_run:
+    label: "1/0 to read pbta-histologies-base.tsv" 
+    value: 0
+    input: integer
 ---
 
 ## Purpose
@@ -26,7 +31,11 @@ set.seed(201910)
 
 ```{r load files}
 root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+if(params$base_run == 0) {
 sample_df <- readr::read_tsv(file.path(root_dir, "data", "pbta-histologies.tsv"), guess_max = 10000)
+} else {
+sample_df <- readr::read_tsv(file.path(root_dir, "data", "pbta-histologies-base.tsv"), guess_max = 10000)
+}
 ```
 
 ## WGS and WXS samples

analyses/independent-samples/results/independent-specimens.rnaseq.primary-plus-stranded.tsv

@@ -37,7 +37,7 @@ PT_1DRAVX4S	BS_Q9V7A95C
 PT_1DSX4VJM	BS_Q13FQ8FV
 PT_1DY2TP9N	BS_E4F1D721
 PT_1EB5KHZX	BS_SBFNFZ8B
-PT_1H2REHT2	BS_WKESC3XN
+PT_1H2REHT2	BS_E0N3PTPN
 PT_1J2DT6MM	BS_GHNJ4CYC
 PT_1KEER2Q1	BS_YY5B2XDD
 PT_1MW98VR1	BS_6H1C1ME9
@@ -78,7 +78,7 @@ PT_2QZJ4T95	BS_B1C6GZ84
 PT_2SCVQ2N6	BS_NGHK9RZP
 PT_2VSDT9CK	BS_G9XE3N9T
 PT_2WA5PM32	BS_86Q14TZG
-PT_2WVW55DA	BS_CXVGG342
+PT_2WVW55DA	BS_D8N31T39
 PT_2YCHME6S	BS_EXYHZ6D4
 PT_2YT37G8P	BS_VW85Q4XJ
 PT_2Z7GVDTM	BS_DV86M0Y7
@@ -95,6 +95,7 @@ PT_39HBKSGG	BS_61E80SD6
 PT_3A0B29QT	BS_264RCK7G
 PT_3A2Q62RD	BS_RGPSEMHC
 PT_3A87PCQK	BS_JXNZYGCR
+PT_3AWKWXEV	BS_SB12W1XT
 PT_3C6QA9MA	BS_FW5ECXXK
 PT_3CHB9PK5	BS_W9N9844Q
 PT_3CVMBGD7	BS_9SJWWYQ4
@@ -147,7 +148,7 @@ PT_50ZFWMZE	BS_X16PENSA
 PT_54MH6Q46	BS_PN2CE34A
 PT_57YP9ABV	BS_YK6VQ9SJ
 PT_596H0BQF	BS_B24PKKQB
-PT_59D00MBQ	BS_TM9MH0RP
+PT_59D00MBQ	BS_ZVWE73JZ
 PT_59FJRPVX	BS_AWH9757B
 PT_5ABCFCSK	BS_A1VEGWTR
 PT_5AF1501D	BS_VMEX27TN
@@ -184,7 +185,7 @@ PT_6MB6RED3	BS_ABYF92Z9
 PT_6MWPJ96F	BS_NPQJ20KX
 PT_6N1QWCXE	BS_4HQ3T2NC
 PT_6PFFSB6D	BS_QBR4WCQ2
-PT_6PP78VNE	BS_M85CXHDV
+PT_6PP78VNE	BS_6VPKXXMR
 PT_6PYNBA9C	BS_NQFH3GZH
 PT_6Q0NPVP3	BS_5JM573JC
 PT_6R7AE0P3	BS_MGAMKKBD
@@ -232,15 +233,17 @@ PT_8CZ6ANE0	BS_273HKCT4
 PT_8ECE2D92	BS_F4E8R9VY
 PT_8FWP7BR3	BS_TMTV769C
 PT_8GBF5MTD	BS_GMJBGBWB
-PT_8GN3TQRM	BS_WAXJY4XQ
+PT_8GN3TQRM	BS_P0QF87WC
 PT_8GW4J4TD	BS_ARFQ1WG3
 PT_8M6W215T	BS_JR5ATB7G
+PT_8P368R5B	BS_FXJY0MNH
 PT_8PV84CNE	BS_74G5K7JF
 PT_8R00BMHH	BS_EBMCTR80
 PT_8RB3EKNP	BS_W9AT0MR7
-PT_8RB7TPS2	BS_HC44ZA0V
+PT_8RB7TPS2	BS_3F4FQJMR
 PT_8SDJXNFR	BS_TZ5D0A7R
 PT_8V3360DR	BS_479S95Q6
+PT_8VRZRZ7R	BS_8QB4S4VA
 PT_8WNA6M94	BS_HBJZR69P
 PT_8XZY6MM1	BS_T4JFN54G
 PT_90W4HCNR	BS_JX449BF5
@@ -253,18 +256,18 @@ PT_99S5BPE3	BS_MT15SGJN
 PT_9A6RPJ97	BS_4D9DD103
 PT_9AHA6KW3	BS_6NTXGQAC
 PT_9B6KWJT2	BS_Z7Y2466H
-PT_9BZETM0M	BS_5P1TN10Z
+PT_9BZETM0M	BS_TV5B86ZD
 PT_9C2G356W	BS_MBSTWZA6
 PT_9CSZBV2P	BS_YBJBSRHV
 PT_9D2N4S5Z	BS_8SKZ7BRN
 PT_9DER14KH	BS_HE57E1RP
-PT_9DMMZ08D	BS_3V3KE3VT
+PT_9DMMZ08D	BS_44A3ES23
 PT_9HMVHQEH	BS_4CP4T22V
 PT_9JT1441X	BS_7GJT4A6A
 PT_9M4CQX3M	BS_ARBQDTT5
 PT_9N0SR1D7	BS_YEW22W35
 PT_9P7P6YAQ	BS_QB7YGKN1
-PT_9PJR0ZK7	BS_6JHXXVR7
+PT_9PJR0ZK7	BS_KE56MMY0
 PT_9S6WMQ92	BS_TW8DQH8J
 PT_9W4WTVFZ	BS_PQVTB6BB
 PT_9YMRNZHH	BS_9NZ2D6AD
@@ -290,7 +293,7 @@ PT_ARCM3PXM	BS_FYRDYBMZ
 PT_ATE3YRH5	BS_BPSTSCBJ
 PT_ATS9XDJ5	BS_JK0VPG1T
 PT_AWBPNFM5	BS_2AR3AP0N
-PT_AWMZ12NP	BS_S9929Z8B
+PT_AWMZ12NP	BS_3H71BH6Q
 PT_AXMVG8QE	BS_K2FHZGTK
 PT_AXVH36AM	BS_1XJ73KBQ
 PT_AYVKQZRB	BS_T0RKFEKR
@@ -381,7 +384,7 @@ PT_DPVW4M1W	BS_SFRQXM76
 PT_DQ3ZCHB6	BS_258RRGDM
 PT_DQT78GS5	BS_37GTVG4N
 PT_DTP4MMRA	BS_2HN96129
-PT_DW2XRPC9	BS_8ZS9F31R
+PT_DW2XRPC9	BS_5CTVXVRX
 PT_DW6V5V8E	BS_EFEZB0ZH
 PT_DXF7ZZQZ	BS_ERJAJ0KA
 PT_E1TRJP8V	BS_HQ5BJ6MW
@@ -414,7 +417,7 @@ PT_EW604JB3	BS_SDA4RMMG
 PT_EXJAEW1M	BS_T1QMEH1N
 PT_EXYXBDGP	BS_4BWB0FA0
 PT_EYHJQQ8E	BS_G7AGNB5G
-PT_EYWDFKA7	BS_TYKJ8G2G
+PT_EYWDFKA7	BS_J4GQPZS0
 PT_EYZ25B99	BS_ZRM0W01M
 PT_EZEMVRVT	BS_F8N6CFQE
 PT_EZS4SRH6	BS_HD4EJYE3
@@ -440,7 +443,7 @@ PT_FWD7NZQ0	BS_M4NVX721
 PT_FXPJM0MW	BS_RRAEQZ97
 PT_FYECBRPP	BS_B1HVNV0T
 PT_FYPWZBH0	BS_2A5R9MEJ
-PT_FZHGKJ0H	BS_2SHWPB5P
+PT_FZHGKJ0H	BS_JBGZ7HHZ
 PT_FZP24XYK	BS_Z8F3GM85
 PT_G16WS1MW	BS_J60G8DMK
 PT_G1QNGVCZ	BS_A14Z8BBK
@@ -503,7 +506,7 @@ PT_J0SZ1SX5	BS_R13X6TMW
 PT_J302B8Y5	BS_K25F4J3V
 PT_J3B812DT	BS_AMQGM1V9
 PT_J4MWGQFQ	BS_Q2T9ZRM0
-PT_J50NZYZF	BS_B9V8RGTA
+PT_J50NZYZF	BS_PSNBFWQV
 PT_J5NSRW1Y	BS_GG9W3J9Y
 PT_JC4DHFJR	BS_QB84TBA3
 PT_JCECCFPB	BS_90B22NGP
@@ -518,6 +521,7 @@ PT_JP1FDKN9	BS_T1DVKKJB
 PT_JPWVCTAJ	BS_R244Z0WX
 PT_JQ45JK94	BS_QH82PBMB
 PT_JSFBMK5V	BS_1A6MQ9ZA
+PT_JT9HH7M6	BS_HE0WJRW6
 PT_JV9G8MFD	BS_9FHSNVS0
 PT_JW2FDK4W	BS_KVAJYZ6F
 PT_JW6FBEFK	BS_3BVVWHP5
@@ -534,7 +538,7 @@ PT_K8ZV7APT	BS_GDHH6T5A
 PT_K94ZVZMX	BS_N4B1SZZH
 PT_KBA2VNA2	BS_9755PSCS
 PT_KBDP8ZCR	BS_M1PVEHCM
-PT_KCTZZA3G	BS_ENKG5GF3
+PT_KCTZZA3G	BS_TAHV8N04
 PT_KDW5HHWQ	BS_C7N3J4NW
 PT_KEQ53KRH	BS_K17VQECG
 PT_KFYJBQB8	BS_52C576HH
@@ -548,16 +552,16 @@ PT_KX84KH6K	BS_52MPKTJH
 PT_KXB1PJV0	BS_3Q0GTSYH
 PT_KZ04SDDS	BS_JS95PE0J
 PT_M04EC74B	BS_31TF0P1N
-PT_M0AP3Z15	BS_Z7PKVY9J
+PT_M0AP3Z15	BS_QEYPFYHD
 PT_M0FVZ88D	BS_THSPSG2Z
 PT_M1RYN7B0	BS_WVW3W6ZB
 PT_M2J30CF7	BS_9GJ23RHH
 PT_M5HDHQNQ	BS_9Q6Z6VJC
 PT_M7NFAC5G	BS_TQ5QHR17
 PT_MA0J8DSN	BS_VTJ9ESSV
 PT_MBAXTJET	BS_401R3KV0
-PT_MDWPRDBT	BS_H0QWRJE2
-PT_MKDQZ17N	BS_QP6MSKRE
+PT_MDWPRDBT	BS_TK84K675
+PT_MKDQZ17N	BS_1J2WQ08M
 PT_MNR94DEV	BS_0WVJYM9R
 PT_MPRBGGEJ	BS_S50KQEXV
 PT_MQHST8YC	BS_DRD9QXR5
@@ -585,7 +589,7 @@ PT_NCDHZ8H8	BS_7C40TRCY
 PT_ND34A6PR	BS_DHA5FMVW
 PT_NDVJE438	BS_4PH1MBGR
 PT_NEB4WEAT	BS_XHCYEE2S
-PT_NESAQHB1	BS_QT3NZ2YZ
+PT_NESAQHB1	BS_QHS3V0GP
 PT_NFDHYPGT	BS_AG4H9S3J
 PT_NGDW8WVP	BS_W41S7B55
 PT_NH8CJ84W	BS_C0XFDP38
@@ -629,7 +633,7 @@ PT_Q38AT6JY	BS_78QX3XDF
 PT_Q3EP24V1	BS_06AMMCXR
 PT_Q90R6M3E	BS_5PJCHF6V
 PT_QAX38GM7	BS_044XZ8ST
-PT_QD6KKKJH	BS_M7QJ8VF0
+PT_QD6KKKJH	BS_7ZV3DPGT
 PT_QDGVJKE0	BS_A0DYVX9J
 PT_QEMT1845	BS_1T19NFJ8
 PT_QEP13FH4	BS_K3ER45RV
@@ -659,7 +663,7 @@ PT_RDJ40M73	BS_1EN5V3XW
 PT_RFB07MZS	BS_TZVFR600
 PT_RFF7MKTC	BS_5YJEPPTP
 PT_RFGZ2JGP	BS_M84H3KXA
-PT_RGX23JFP	BS_ZZWMD6FA
+PT_RGX23JFP	BS_PQ6QEVE8
 PT_RH59ET3M	BS_EFE4YEK3
 PT_RJ1TJ2KH	BS_4E1G7E3G
 PT_RJ98S3KZ	BS_DFWFBYSN
@@ -676,17 +680,18 @@ PT_RV0RDER2	BS_XKKB4MZV
 PT_RX1EWBP9	BS_996ZS2A4
 PT_RXJZ3C5G	BS_8RCR7Y4B
 PT_RXT6KRR6	BS_NFRXNAFE
+PT_RYMG3M91	BS_D7XRFE0R
 PT_S0PBN4M7	BS_RWJZFTP9
 PT_S0Q27J13	BS_Z8YZ6QGS
 PT_S21ZTKPS	BS_014EVM2D
 PT_S2ASFBP7	BS_A7MC2KR2
 PT_S2BEPYQ0	BS_JRYJGYC4
 PT_S2CXXZCF	BS_Y0PCBNJV
-PT_S2SQJVGK	BS_S458NMKH
+PT_S2SQJVGK	BS_JFR750KD
 PT_S3FJSBJT	BS_ZV9Z3SY6
 PT_S4A0R1PM	BS_M15PW2N0
 PT_S4H6KA09	BS_07ANYSYQ
-PT_S4YNE17X	BS_VXEFKW5P
+PT_S4YNE17X	BS_GR46VD0Q
 PT_S7WJ99PC	BS_AVYNZHSB
 PT_S8E3281G	BS_TNRHHYNC
 PT_SA94083W	BS_8S86CM61
@@ -748,9 +753,10 @@ PT_VVCN8DXT	BS_X4X1SFSE
 PT_VWZZTK38	BS_TXZ7KHTQ
 PT_VY45XTT7	BS_AHEFXG7W
 PT_VZTTTP3Q	BS_E4QK839R
-PT_W17NV5YG	BS_V4W81SFC
+PT_W17NV5YG	BS_TCGEZJ5F
 PT_W3FSA7NH	BS_VARR255N
 PT_W4XVT4AJ	BS_MKM0EEN1
+PT_W5GP3F6B	BS_KABQQA0T
 PT_W6AWJJK7	BS_478TN841
 PT_W6CW60K9	BS_NGY0TE6S
 PT_W7FK539G	BS_XBQZYS8G
@@ -775,6 +781,7 @@ PT_X1PRY0FC	BS_FJWZ3M7V
 PT_X1XVE1XX	BS_A87NPZAP
 PT_X648RVMK	BS_N6N147BY
 PT_X71D7G5S	BS_C6ZZ3FY5
+PT_X7HC5YCY	BS_FN07P04C
 PT_X84SD608	BS_9HA238XS
 PT_X8S0H6TG	BS_1N9XZXGE
 PT_X8SK8120	BS_DGTPWJ59
@@ -796,7 +803,7 @@ PT_XX2VW3D9	BS_VJVDJABP
 PT_XXZHRPNM	BS_MF9X3PKH
 PT_XY404K0D	BS_8F9BDWY4
 PT_Y4FN0XN1	BS_4NWHYH53
-PT_Y572BRC1	BS_EN2VK7NY
+PT_Y572BRC1	BS_V0Q1G94N
 PT_Y5KY6KN9	BS_4QW2S1Q8
 PT_Y660CKCB	BS_XG0DBWVT
 PT_Y6Y9JJ9P	BS_0WQJP6ZG
@@ -824,6 +831,7 @@ PT_YXZPWFVB	BS_P78SMRBS
 PT_YY7CRV21	BS_Z2NWPQKF
 PT_YZ8A8A36	BS_GSVCN2XC
 PT_YZME6QCY	BS_68BW2163
+PT_Z4BF2NSB	BS_SHJA4MR0
 PT_Z4GS3ZQQ	BS_EVCAC3NH
 PT_Z4PJA6KT	BS_6WP1FHTE
 PT_Z7YJ7MSM	BS_F6V1Y4QS