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thelovelab / tximport

Transcript quantification import for modular pipelines
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Transcript expression collapsing to gene-level expression #26

Closed beginner984 closed 5 years ago

beginner984 commented 5 years ago

Sorry, I have raw read counts from FeatureCounts, can I still use tximport to collapsing transcrip expression to gene level?

mikelove commented 5 years ago

No that’s not a use case

beginner984 commented 5 years ago

Sorry, I have this matrix from HTSeq, can I use your software to convert this HTSeq count from ENSG IDs with counts to HGNC gene symbols with counts ?

head(SummarizedExperiment::assay(data)) TCGA-L5-A4OG-11A-12R-A260-31 TCGA-IC-A6RE-11A-12R-A336-31 TCGA-L5-A4OJ-11A-12R-A260-31 ENSG00000000003 1818 4596 2732 ENSG00000000005 0 3 6 ENSG00000000419 1436 751 1500 ENSG00000000457 1175 840 992 ENSG00000000460 242 205 256 ENSG00000000938 536 253 331 TCGA-L5-A4OO-11A-12R-A260-31 TCGA-V5-AASX-11A-11R-A38D-31 TCGA-L5-A4OF-11A-12R-A260-31 ENSG00000000003 1075 1829 1282 ENSG00000000005 3 1 1 ENSG00000000419 1139 1703 1105 ENSG00000000457 726 1903 800 ENSG00000000460 123 416 358 ENSG00000000938 372 92 136 TCGA-L5-A4OR-11A-11R-A260-31 TCGA-L5-A43C-11A-11R-A24K-31 TCGA-L5-A4OQ-11A-12R-A260-31 ENSG00000000003 1886 1275 1214 ENSG00000000005 2 0 12 ENSG00000000419 1117 928 2152 ENSG00000000457 617 594 1551 ENSG00000000460 78 80 309 ENSG00000000938 142 152 1635 TCGA-V5-A7RE-11A-11R-A354-31 TCGA-IC-A6RF-11A-21R-A336-31 ENSG00000000003 1548 4458 ENSG00000000005 3 3 ENSG00000000419 2115 1835 ENSG00000000457 1306 766 ENSG00000000460 514 150 ENSG00000000938 514 133

mikelove commented 5 years ago

No that’s not what tximport does. We only take input from the methods listed in the help page: For usage questions please post to the Bioc support site in the future.