Sparse Matrix Duplicated Rownames Error

[Pacomito]

Issue From Guillaume Bourmeau: "" Hello Pacome,

But I am hitting a wall currently, because I input 10X sparse matrix files (the 3 as requested per sample). Unfortunately it doesn't work because of row duplicates :

Here is the error message:

[1] "Feature annotation..."
ChromSCape::feature_annotation_scExp - Selecting hg38 genes from Gencode.
Avis : non-unique values when setting 'row.names': ‘chr1_111498633_111508633’, ‘chr1_43645149_43655149’, ‘chr1_46171488_46181488’, ‘chr1_85573250_85583250’, ‘chr11_66611626_66621626’, ‘chr12_2807902_2817902’, ‘chr12_4268762_4278762’, ‘chr14_103557962_103567962’, ‘chr14_95658256_95668256’, ‘chr15_43794133_43804133’, ‘chr15_64836883_64846883’, ‘chr15_68925525_68935525’, ‘chr16_56677470_56687470’, ‘chr17_10724777_10734777’, ‘chr17_7399097_7409097’, ‘chr19_12479816_12489816’, ‘chr19_16623204_16633204’, ‘chr19_40766648_40776648’, ‘chr19_45597212_45607212’, ‘chr19_56835726_56845726’, ‘chr2_169474480_169484480’, ‘chr2_3553333_3563333’, ‘chr2_99136485_99146485’, ‘chr20_3154865_3164865’, ‘chr21_33224901_33234901’, ‘chr22_38789143_38799143’, ‘chr3_170413868_170423868’, ‘chr4_38851817_38861817’, ‘chr6_26194293_26204293’, ‘chr7_42927174_42937174’, ‘chr7_6479190_6489190’, ‘chr9_133 […tronqué]
Chronométrage arrêté à : 0.95 0.034 0.996
Avis : Error in .rowNamesDF<-: les duplications dans 'row.names' ne sont pas autorisées

There is not much flexibility for me to try something else, except using another input format, but I wanted to give a shot with this first...

Thanks a lot, Best regards, Guillaume Bourmeau """

[Pacomito]

Hello Guillaume,

Thanks you for your issue, I fixed the first issue of duplicated rownames, please give it a try by re-installing the github version of chromscape:

devtools::install_github("vallotlab/ChromSCape")

and try again to load the sparse matrix.

Does it work now ?

For the bioconductor version, this will be fixed for next Bioconductor release.

Best, Pacôme