Load sample data from file and rename samples using names of samples and an optional order
Source:R/targets_misc.R
sample_data_with_new_names.Rd
Useful for targets bioinformatic pipeline.
Arguments
- file_path
(required) a path to the sample_data file
- names_of_samples
(required) a vector of sample names
- samples_order
Optional numeric vector to sort sample names
- ...
Other arguments passed on to
utils::read.delim()function.
Examples
sam_file <- system.file("extdata", "sam_data.csv", package = "MiscMetabar")
sample_data_with_new_names(sam_file, paste0("Samples_", seq(1, 185)))
#> X Sample_names Tree_name
#> Samples_1 A10-005-B_S188_MERGED.fastq.gz A10-005-B_S188 A10-005
#> Samples_2 A10-005-H_S189_MERGED.fastq.gz A10-005-H_S189 A10-005
#> Samples_3 A10-005-M_S190_MERGED.fastq.gz A10-005-M_S190 A10-005
#> Samples_4 A12-007_S191_MERGED.fastq.gz A12-007_S191 A12-007
#> Samples_5 A12-007-B_S2_MERGED.fastq.gz A12-007-B_S2 A12-007
#> Samples_6 A15-004_S3_MERGED.fastq.gz A15-004_S3 A15-004
#> Samples_7 A8-005_S4_MERGED.fastq.gz A8-005_S4 A8-005
#> Samples_8 A9-012_S5_MERGED.fastq.gz A9-012_S5 A9-012
#> Samples_9 AB29-ABMX-H_S6_MERGED.fastq.gz AB29-ABMX-H_S6 AB29-abm-X
#> Samples_10 AC27-013_S7_MERGED.fastq.gz AC27-013_S7 AC27-013
#> Samples_11 AC29033_S8_MERGED.fastq.gz AC29033_S8 AC29-033
#> Samples_12 AD26-005-B_S9_MERGED.fastq.gz AD26-005-B_S9 AD26-005
#> Samples_13 AD26-005-H_S10_MERGED.fastq.gz AD26-005-H_S10 AD26-005
#> Samples_14 AD26-005-M_S11_MERGED.fastq.gz AD26-005-M_S11 AD26-005
#> Samples_15 AD30-ABMX-M_S12_MERGED.fastq.gz AD30-ABMX-M_S12 AD30-abm-X
#> Samples_16 AD32-007-M_S13_MERGED.fastq.gz AD32-007-M_S13 AD32-007
#> Samples_17 ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-B_S14 AD30-abm-X
#> Samples_18 ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-H_S15 AD30-abm-X
#> Samples_19 ADABM30X-M_S16_MERGED.fastq.gz ADABM30X-M_S16 AD30-abm-X
#> Samples_20 AE30-ABM507_S17_MERGED.fastq.gz AE30-ABM507_S17 AE30-abm507
#> Samples_21 B17-014_S18_MERGED.fastq.gz B17-014_S18 BI7-014
#> Samples_22 B18-006-B_S19_MERGED.fastq.gz B18-006-B_S19 B18-006
#> Samples_23 BA16-036bis_S20_MERGED.fastq.gz BA16-036bis_S20 BA16-036
#> Samples_24 BA17-050-B_S21_MERGED.fastq.gz BA17-050-B_S21 BA17-050
#> Samples_25 BB19-006-H_S22_MERGED.fastq.gz BB19-006-H_S22 BB19-006
#> Samples_26 BB6-019-B_S23_MERGED.fastq.gz BB6-019-B_S23 BB6-019
#> Samples_27 BB6-019-H_S24_MERGED.fastq.gz BB6-019-H_S24 BB6-019
#> Samples_28 BB6-019-M_S25_MERGED.fastq.gz BB6-019-M_S25 BB6-019
#> Samples_29 BD14-021_S26_MERGED.fastq.gz BD14-021_S26 BD14-021
#> Samples_30 BE9-006-B_S27_MERGED.fastq.gz BE9-006-B_S27 BE9-006
#> Samples_31 BE9-006-H_S28_MERGED.fastq.gz BE9-006-H_S28 BE9-006
#> Samples_32 BE9-006-M_S29_MERGED.fastq.gz BE9-006-M_S29 BE9-006
#> Samples_33 BG7-010-B_S30_MERGED.fastq.gz BG7-010-B_S30 BG7-010
#> Samples_34 BG7-010-H_S31_MERGED.fastq.gz BG7-010-H_S31 BG7-010
#> Samples_35 BG7-010-M_S32_MERGED.fastq.gz BG7-010-M_S32 BG7-010
#> Samples_36 BH9-021_S33_MERGED.fastq.gz BH9-021_S33 BH9-021
#> Samples_37 BJ17-007-M_S34_MERGED.fastq.gz BJ17-007-M_S34 BJ17-007
#> Samples_38 BJ8-ABM-003_S35_MERGED.fastq.gz BJ8-ABM-003_S35 BJ8abm003
#> Samples_39 BL7-006-B_S36_MERGED.fastq.gz BL7-006-B_S36 BL7-006
#> Samples_40 BL7-006-H_S37_MERGED.fastq.gz BL7-006-H_S37 BL7-006
#> Samples_41 BL7-006-M_S38_MERGED.fastq.gz BL7-006-M_S38 BL7-006
#> Samples_42 BN11-041_S39_MERGED.fastq.gz BN11-041_S39 BN11-041
#> Samples_43 BN9-002_S40_MERGED.fastq.gz BN9-002_S40 BN9-002
#> Samples_44 BO8-002_S41_MERGED.fastq.gz BO8-002_S41 BO8-002
#> Samples_45 BO8-005_S42_MERGED.fastq.gz BO8-005_S42 BO8-005
#> Samples_46 BP11-001-B_S43_MERGED.fastq.gz BP11-001-B_S43 BP11-001
#> Samples_47 BP11-001-H_S44_MERGED.fastq.gz BP11-001-H_S44 BP11-001
#> Samples_48 BP11-001-M_S45_MERGED.fastq.gz BP11-001-M_S45 BP11-001
#> Samples_49 BP12-025-B_S46_MERGED.fastq.gz BP12-025-B_S46 BP12-025
#> Samples_50 BP14-006_S47_MERGED.fastq.gz BP14-006_S47 BP14-006
#> Samples_51 BQ3-019_S48_MERGED.fastq.gz BQ3-019_S48 BQ3-019
#> Samples_52 BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-B_S49 BQ4-018
#> Samples_53 BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-H_S50 BQ4-018
#> Samples_54 BQ4-018-M_S51_MERGED.fastq.gz BQ4-018-M_S51 BQ4-018
#> Samples_55 BQ9ABM-002_S52_MERGED.fastq.gz BQ9ABM-002_S52 BQ9abm002
#> Samples_56 BR8-005_S53_MERGED.fastq.gz BR8-005_S53 BR8-005
#> Samples_57 BS14-006_S54_MERGED.fastq.gz BS14-006_S54 BS14-006
#> Samples_58 BT-006-M_S55_MERGED.fastq.gz BT-006-M_S55 BT7-006
#> Samples_59 BT7-006_S56_MERGED.fastq.gz BT7-006_S56 BT7-006
#> Samples_60 BV11-002-B_S57_MERGED.fastq.gz BV11-002-B_S57 BU11-002
#> Samples_61 BV11-002-H_S58_MERGED.fastq.gz BV11-002-H_S58 BU11-002
#> Samples_62 BV11-002-M_S59_MERGED.fastq.gz BV11-002-M_S59 BU11-002
#> Samples_63 BW8-003_S60_MERGED.fastq.gz BW8-003_S60 BW8-003
#> Samples_64 C1-001_S61_MERGED.fastq.gz C1-001_S61 C1-001
#> Samples_65 C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-B_S62 C21-nv-1
#> Samples_66 C21-NV1-H_S63_MERGED.fastq.gz C21-NV1-H_S63 C21-nv-1
#> Samples_67 C21-NV1-M_S64_MERGED.fastq.gz C21-NV1-M_S64 C21-nv-1
#> Samples_68 C9-005_S65_MERGED.fastq.gz C9-005_S65 C9-005
#> Samples_69 CA12-024_S66_MERGED.fastq.gz CA12-024_S66 CA12-024
#> Samples_70 CA9-027_S67_MERGED.fastq.gz CA9-027_S67 CA9-027
#> Samples_71 CA9-X_S68_MERGED.fastq.gz CA9-X_S68 CA9-X
#> Samples_72 CB8-019-B_S69_MERGED.fastq.gz CB8-019-B_S69 CB8-019
#> Samples_73 CB8-019-H_S70_MERGED.fastq.gz CB8-019-H_S70 CB8-019
#> Samples_74 CB8-019-M_S71_MERGED.fastq.gz CB8-019-M_S71 CB8-019
#> Samples_75 CB9-013_S72_MERGED.fastq.gz CB9-013_S72 CB9-013
#> Samples_76 CC3-044_S73_MERGED.fastq.gz CC3-044_S73 CC3-044
#> Samples_77 CC8-003_S74_MERGED.fastq.gz CC8-003_S74 CC8-003
#> Samples_78 D17-011_S77_MERGED.fastq.gz D17-011_S77 D17-011
#> Samples_79 D18-003-B_S78_MERGED.fastq.gz D18-003-B_S78 D18-003
#> Samples_80 D18-003-H_S79_MERGED.fastq.gz D18-003-H_S79 D18-003
#> Samples_81 D18-003-M_S80_MERGED.fastq.gz D18-003-M_S80 D18-003
#> Samples_82 D22-NVABM1_S81_MERGED.fastq.gz D22-NVABM1_S81 D22-nvabm-1
#> Samples_83 D61-010-B_S82_MERGED.fastq.gz D61-010-B_S82 DG1-010
#> Samples_84 D9-027-B_S83_MERGED.fastq.gz D9-027-B_S83 D9-027
#> Samples_85 D9-027-H_S84_MERGED.fastq.gz D9-027-H_S84 D9-027
#> Samples_86 D9-027-M_S85_MERGED.fastq.gz D9-027-M_S85 D9-027
#> Samples_87 DBM-ABM-001_S86_MERGED.fastq.gz DBM-ABM-001_S86 DB1abm001
#> Samples_88 DJ2-008-B_S87_MERGED.fastq.gz DJ2-008-B_S87 DJ2-008
#> Samples_89 DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-H_S88 DJ2-008
#> Samples_90 DJ2-008-M_S89_MERGED.fastq.gz DJ2-008-M_S89 DJ2-008
#> Samples_91 DP4-ABM001_S90_MERGED.fastq.gz DP4-ABM001_S90 DP4abm001
#> Samples_92 DS1-ABM002-B_S91_MERGED.fastq.gz DS1-ABM002-B_S91 DS1abm002
#> Samples_93 DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-H_S92 DS1abm002
#> Samples_94 DS1-ABM002-M_S93_MERGED.fastq.gz DS1-ABM002-M_S93 DS1abm002
#> Samples_95 DU3-045-B_S94_MERGED.fastq.gz DU3-045-B_S94 DU3-045
#> Samples_96 DW4-007_S95_MERGED.fastq.gz DW4-007_S95 DW4-007
#> Samples_97 DY5-004-B_S96_MERGED.fastq.gz DY5-004-B_S96 DY5-004
#> Samples_98 DY5-004-H_S97_MERGED.fastq.gz DY5-004-H_S97 DY5-004
#> Samples_99 DY5-004-M_S98_MERGED.fastq.gz DY5-004-M_S98 DY5-004
#> Samples_100 DZ6-ABM-001_S99_MERGED.fastq.gz DZ6-ABM-001_S99 DZ6abm001
#> Samples_101 E9-009-B_S100_MERGED.fastq.gz E9-009-B_S100 E9-009
#> Samples_102 E9-009-H_S101_MERGED.fastq.gz E9-009-H_S101 E9-009
#> Samples_103 E9-009-M_S102_MERGED.fastq.gz E9-009-M_S102 E9-009
#> Samples_104 EA5-ABM-001_S103_MERGED.fastq.gz EA5-ABM-001_S103 EAabm001
#> Samples_105 EC2-013-B_S104_MERGED.fastq.gz EC2-013-B_S104 EC2-013
#> Samples_106 F6-ABM-001_S105_MERGED.fastq.gz F6-ABM-001_S105 F6abm001
#> Samples_107 F7-015-M_S106_MERGED.fastq.gz F7-015-M_S106 F7-015
#> Samples_108 FOMES19-H_S108_MERGED.fastq.gz FOMES19-H_S108 FOMES19
#> Samples_109 FOMES19-M_S109_MERGED.fastq.gz FOMES19-M_S109 FOMES19
#> Samples_110 H10-018-M_S110_MERGED.fastq.gz H10-018-M_S110 H10-018
#> Samples_111 H24-NVABM1-H_S111_MERGED.fastq.gz H24-NVABM1-H_S111 H24-nvabm-1
#> Samples_112 J18-004-B_S114_MERGED.fastq.gz J18-004-B_S114 J18-004
#> Samples_113 J18-004-H_S115_MERGED.fastq.gz J18-004-H_S115 J18-004
#> Samples_114 J18-004-M_S116_MERGED.fastq.gz J18-004-M_S116 J18-004
#> Samples_115 K18-002-H_S117_MERGED.fastq.gz K18-002-H_S117 K18-002
#> Samples_116 K26-NVABM1_S118_MERGED.fastq.gz K26-NVABM1_S118 K26-nvamb-1
#> Samples_117 L19X-B_S119_MERGED.fastq.gz L19X-B_S119 L19-X
#> Samples_118 L19X-H_S120_MERGED.fastq.gz L19X-H_S120 L19-X
#> Samples_119 L19X-M_S121_MERGED.fastq.gz L19X-M_S121 L19-X
#> Samples_120 L23-002-B_S122_MERGED.fastq.gz L23-002-B_S122 L23-002
#> Samples_121 L23-002-H_S123_MERGED.fastq.gz L23-002-H_S123 L23-002
#> Samples_122 L23-002-M_S124_MERGED.fastq.gz L23-002-M_S124 L23-002
#> Samples_123 M22-001_S125_MERGED.fastq.gz M22-001_S125 M22-001
#> Samples_124 N19X-B_S126_MERGED.fastq.gz N19X-B_S126 N19-X
#> Samples_125 N19X-H_S127_MERGED.fastq.gz N19X-H_S127 N19-X
#> Samples_126 N19X-M_S128_MERGED.fastq.gz N19X-M_S128 N19-X
#> Samples_127 N22-001-B_S129_MERGED.fastq.gz N22-001-B_S129 M22-001
#> Samples_128 N23-002-B_S130_MERGED.fastq.gz N23-002-B_S130 N23-002
#> Samples_129 N23-002-H_S131_MERGED.fastq.gz N23-002-H_S131 N23-002
#> Samples_130 N23-002-M_S132_MERGED.fastq.gz N23-002-M_S132 N23-002
#> Samples_131 N25-ABMX_S133_MERGED.fastq.gz N25-ABMX_S133 N25-abm-X
#> Samples_132 NVABM-0058_S134_MERGED.fastq.gz NVABM-0058_S134 nvabm0058
#> Samples_133 NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0163-H_S135 nvabm0163
#> Samples_134 NVABM-0397_S138_MERGED.fastq.gz NVABM-0397_S138 nvabm0397
#> Samples_135 NVABM0216_S136_MERGED.fastq.gz NVABM0216_S136 nvabm0216
#> Samples_136 NVABM0244-M_S137_MERGED.fastq.gz NVABM0244-M_S137 nvabm0244
#> Samples_137 O20-X-B_S139_MERGED.fastq.gz O20-X-B_S139 O20-X
#> Samples_138 O20-X-H_S140_MERGED.fastq.gz O20-X-H_S140 O20-X
#> Samples_139 O20-X-M_S141_MERGED.fastq.gz O20-X-M_S141 O20-X
#> Samples_140 O21-007-B_S142_MERGED.fastq.gz O21-007-B_S142 O21-007
#> Samples_141 O21-007-H_S143_MERGED.fastq.gz O21-007-H_S143 O21-007
#> Samples_142 O21-007-M_S144_MERGED.fastq.gz O21-007-M_S144 O21-007
#> Samples_143 O24-003-B_S145_MERGED.fastq.gz O24-003-B_S145 O24-003
#> Samples_144 O24-003-H_S146_MERGED.fastq.gz O24-003-H_S146 O24-003
#> Samples_145 O24-003-M_S147_MERGED.fastq.gz O24-003-M_S147 O24-003
#> Samples_146 O26-004-B_S148_MERGED.fastq.gz O26-004-B_S148 O26-004
#> Samples_147 O26-004-H_S149_MERGED.fastq.gz O26-004-H_S149 O26-004
#> Samples_148 O26-004-M_S150_MERGED.fastq.gz O26-004-M_S150 O26-004
#> Samples_149 O27-012_S151_MERGED.fastq.gz O27-012_S151 O27-012
#> Samples_150 O9-005-B_S152_MERGED.fastq.gz O9-005-B_S152 C9-005
#> Samples_151 P19-023-M_S153_MERGED.fastq.gz P19-023-M_S153 P19-023
#> Samples_152 P27-015-M_S154_MERGED.fastq.gz P27-015-M_S154 P27-015
#> Samples_153 P27-ABM001_S155_MERGED.fastq.gz P27-ABM001_S155 P27-abm001
#> Samples_154 Q27-ABM003-B_S156_MERGED.fastq.gz Q27-ABM003-B_S156 Q27-abm003
#> Samples_155 R25-ABMX_S157_MERGED.fastq.gz R25-ABMX_S157 R25-abm-X
#> Samples_156 R28-008-B_S158_MERGED.fastq.gz R28-008-B_S158 R28-008
#> Samples_157 R28-008-H_S159_MERGED.fastq.gz R28-008-H_S159 R28-008
#> Samples_158 R28-008-M_S160_MERGED.fastq.gz R28-008-M_S160 R28-008
#> Samples_159 T28-011_S161_MERGED.fastq.gz T28-011_S161 T28-011
#> Samples_160 T28-ABM602-B_S162_MERGED.fastq.gz T28-ABM602-B_S162 T28-abm602
#> Samples_161 U27-ABM002_S163_MERGED.fastq.gz U27-ABM002_S163 U27-abm002
#> Samples_162 W25-ABMX_S164_MERGED.fastq.gz W25-ABMX_S164 W25-abm-X
#> Samples_163 W26-001-B_S165_MERGED.fastq.gz W26-001-B_S165 W26-001
#> Samples_164 W26-001-H_S166_MERGED.fastq.gz W26-001-H_S166 W26-001
#> Samples_165 W26-001-M_S167_MERGED.fastq.gz W26-001-M_S167 W26-001
#> Samples_166 W30-006_S168_MERGED.fastq.gz W30-006_S168 W30-006
#> Samples_167 W9-025-M_S169_MERGED.fastq.gz W9-025-M_S169 W29-025
#> Samples_168 X24-009-B_S170_MERGED.fastq.gz X24-009-B_S170 X24-009
#> Samples_169 X24-009-H_S171_MERGED.fastq.gz X24-009-H_S171 X24-009
#> Samples_170 X24-009-M_S172_MERGED.fastq.gz X24-009-M_S172 X24-009
#> Samples_171 X24-010_S173_MERGED.fastq.gz X24-010_S173 X24-010
#> Samples_172 X29-004-B_S174_MERGED.fastq.gz X29-004-B_S174 X29-004
#> Samples_173 X29-004-H_S175_MERGED.fastq.gz X29-004-H_S175 X29-004
#> Samples_174 X29-004-M_S176_MERGED.fastq.gz X29-004-M_S176 X29-004
#> Samples_175 Y21-ABM484-H_S177_MERGED.fastq.gz Y21-ABM484-H_S177 Y31-abm484
#> Samples_176 Y28-002-B_S178_MERGED.fastq.gz Y28-002-B_S178 Y28-002
#> Samples_177 Y28-002-H_S179_MERGED.fastq.gz Y28-002-H_S179 Y28-002
#> Samples_178 Y28-002-M_S180_MERGED.fastq.gz Y28-002-M_S180 Y28-002
#> Samples_179 Y29-007-B_S181_MERGED.fastq.gz Y29-007-B_S181 Y29-007
#> Samples_180 Y29-007-H_S182_MERGED.fastq.gz Y29-007-H_S182 Y29-007
#> Samples_181 Y29-007-M_S183_MERGED.fastq.gz Y29-007-M_S183 Y29-007
#> Samples_182 Y31-ABM484-B_S184_MERGED.fastq.gz Y31-ABM484-B_S184 Y31-abm484
#> Samples_183 Z29-001-H_S185_MERGED.fastq.gz Z29-001-H_S185 Z29-001
#> Samples_184 Z30-002_S186_MERGED.fastq.gz Z30-002_S186 Z30-002
#> Samples_185 Z30-ABM560-M_S187_MERGED.fastq.gz Z30-ABM560-M_S187 Z30-abm560
#> Sample_id Height Diameter Time
#> Samples_1 188 Low 52 15
#> Samples_2 189 High 52 15
#> Samples_3 190 Middle 52 15
#> Samples_4 191 <NA> 28,4 0
#> Samples_5 2 Low 28,4 0
#> Samples_6 3 <NA> 30,7 0
#> Samples_7 4 <NA> 32,8 0
#> Samples_8 5 <NA> 33,3 0
#> Samples_9 6 High 99 5
#> Samples_10 7 <NA> 32 15
#> Samples_11 8 <NA> 55,4 15
#> Samples_12 9 Low 115,5 15
#> Samples_13 10 High 115,5 15
#> Samples_14 11 Middle 115,5 15
#> Samples_15 12 Middle - 5
#> Samples_16 13 Middle 52 NA
#> Samples_17 14 Low - 5
#> Samples_18 15 High - 5
#> Samples_19 16 Middle - 5
#> Samples_20 17 <NA> 10 5
#> Samples_21 18 <NA> 21,5 NA
#> Samples_22 19 Low 32,5 10
#> Samples_23 20 <NA> 40,3 15
#> Samples_24 21 Low 30 10
#> Samples_25 22 High 37,5 15
#> Samples_26 23 Low 33,8 5
#> Samples_27 24 High 33,8 5
#> Samples_28 25 Middle 33,8 5
#> Samples_29 26 <NA> 32,4 5
#> Samples_30 27 Low 23,1 0
#> Samples_31 28 High 23,1 0
#> Samples_32 29 Middle 23,1 0
#> Samples_33 30 Low 32 0
#> Samples_34 31 High 32 0
#> Samples_35 32 Middle 32 0
#> Samples_36 33 <NA> 44,3 0
#> Samples_37 34 Middle 32 5
#> Samples_38 35 <NA> 40 15
#> Samples_39 36 Low 35,6 0
#> Samples_40 37 High 35,6 0
#> Samples_41 38 Middle 35,6 0
#> Samples_42 39 <NA> 38,3 NA
#> Samples_43 40 <NA> 32,5 0
#> Samples_44 41 <NA> 26,5 10
#> Samples_45 42 <NA> 23 0
#> Samples_46 43 Low 47,5 15
#> Samples_47 44 High 47,5 15
#> Samples_48 45 Middle 47,5 15
#> Samples_49 46 Low 64,5 10
#> Samples_50 47 <NA> 25,3 10
#> Samples_51 48 <NA> 80 15
#> Samples_52 49 Low 34 0
#> Samples_53 50 High 34 0
#> Samples_54 51 Middle 34 0
#> Samples_55 52 <NA> 40 15
#> Samples_56 53 <NA> 36,8 0
#> Samples_57 54 <NA> 35 15
#> Samples_58 55 Middle 41 0
#> Samples_59 56 <NA> 41 0
#> Samples_60 57 Low 33 5
#> Samples_61 58 High 33 5
#> Samples_62 59 Middle 33 5
#> Samples_63 60 <NA> 38,2 0
#> Samples_64 61 <NA> 43 10
#> Samples_65 62 Low 30 0
#> Samples_66 63 High 30 0
#> Samples_67 64 Middle 30 0
#> Samples_68 65 <NA> 39 5
#> Samples_69 66 <NA> 18,3 NA
#> Samples_70 67 <NA> 23,4 0
#> Samples_71 68 <NA> - 15
#> Samples_72 69 Low 33,3 0
#> Samples_73 70 High 33,3 0
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