Hi there,
What exactly is the format of the cells argument in the function FeatureMatrix? I am passing the barcode names from CountFragments, and FeatureMatrix returns NULL.
In the example below, all barcodes that I am interested in filtering (target_cells) are present in the large matrix out_all. But whenever I pass cells = target_cells in FeatureMatrix, I get NULL as the output.
> library(Signac)
> library(GenomicRanges)
> frag_path <- '~/fragments.tsv.gz'
> peak_path <- '~/peaks.bed'
> frag_object <- CreateFragmentObject(frag_path,verbose = TRUE)
Computing hash
>
> frag_counts <- CountFragments(fragments = frag_path)
>
> target_cells <- frag_counts[frag_counts$frequency_count > 1000, "CB"]
>
> head(target_cells)
[1] "CTAGGATTCTTGTGCC-1" "CAGGATTGTTACGGAG-1" "GCGCCAAGTCACAGTT-1" "GCACGCAAGTACGCGA-1" "TGCTATTCATGGCCCA-1"
[6] "CCCTGATCATCATCGA-1"
> length(target_cells)
[1] 57
>
> feat <- GenomicRanges::makeGRangesFromDataFrame(df = read.table(peak_path),
+ seqnames.field = 'V1',
+ start.field = 'V2',
+ end.field = 'V3')
> feat
GRanges object with 8024 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 4807482-4808370 *
[2] chr1 4857304-4858176 *
[3] chr1 5022457-5023326 *
[4] chr1 7088433-7089350 *
[5] chr1 7397617-7398457 *
... ... ... ...
[8020] chrY 90808457-90809289 *
[8021] chrY 90812575-90813471 *
[8022] JH584304.1 59182-60057 *
[8023] GL456216.1 15533-16423 *
[8024] GL456216.1 16735-17567 *
-------
seqinfo: 23 sequences from an unspecified genome; no seqlengths
>
> out_all <- FeatureMatrix(fragments = frag_object,
+ features = feat,
+ verbose = TRUE)
Extracting reads overlapping genomic regions
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=11s
>
> all(target_cells %in% colnames(out_all))
[1] TRUE
>
> out_cells <- FeatureMatrix(fragments = frag_object,
+ features = feat,
+ verbose = TRUE,
+ cells = target_cells)
>
> out_cells
NULL
>
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /stornext/System/data/apps/R/R-4.1.1/lib64/R/lib/libRblas.so
LAPACK: /stornext/System/data/apps/R/R-4.1.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0
[6] Signac_1.4.0 devtools_2.4.2 usethis_2.0.1
loaded via a namespace (and not attached):
[1] fastmatch_1.1-3 plyr_1.8.6 igraph_1.2.6 lazyeval_0.2.2
[5] splines_4.1.1 BiocParallel_1.26.2 listenv_0.8.0 SnowballC_0.7.0
[9] scattermore_0.7 ggplot2_3.3.5 digest_0.6.27 htmltools_0.5.2
[13] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0 tensor_1.5
[17] cluster_2.1.2 ROCR_1.0-11 remotes_2.4.0 globals_0.14.0
[21] Biostrings_2.60.2 matrixStats_0.61.0 docopt_0.7.1 spatstat.sparse_2.0-0
[25] prettyunits_1.1.1 colorspace_2.0-2 ggrepel_0.9.1 dplyr_1.0.7
[29] sparsesvd_0.2 callr_3.7.0 crayon_1.4.1 RCurl_1.98-1.5
[33] jsonlite_1.7.2 spatstat.data_2.1-0 survival_3.2-13 zoo_1.8-9
[37] glue_1.4.2 polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.38.0
[41] XVector_0.32.0 leiden_0.3.9 pkgbuild_1.2.0 future.apply_1.8.1
[45] abind_1.4-5 scales_1.1.1 DBI_1.1.1 miniUI_0.1.1.1
[49] Rcpp_1.0.7 viridisLite_0.4.0 xtable_1.8-4 reticulate_1.22
[53] spatstat.core_2.3-0 htmlwidgets_1.5.4 httr_1.4.2 RColorBrewer_1.1-2
[57] ellipsis_0.3.2 Seurat_4.0.4 ica_1.0-2 farver_2.1.0
[61] pkgconfig_2.0.3 ggseqlogo_0.1 uwot_0.1.10 deldir_0.2-10
[65] utf8_1.2.2 tidyselect_1.1.1 rlang_0.4.11 reshape2_1.4.4
[69] later_1.3.0 munsell_0.5.0 tools_4.1.1 cachem_1.0.6
[73] cli_3.0.1 generics_0.1.0 ggridges_0.5.3 stringr_1.4.0
[77] fastmap_1.1.0 goftest_1.2-2 processx_3.5.2 fs_1.5.0
[81] fitdistrplus_1.1-5 purrr_0.3.4 RANN_2.6.1 pbapply_1.5-0
[85] future_1.22.1 nlme_3.1-153 mime_0.11 slam_0.1-48
[89] RcppRoll_0.3.0 compiler_4.1.1 rstudioapi_0.13 plotly_4.9.4.1
[93] png_0.1-7 testthat_3.0.4 spatstat.utils_2.2-0 tibble_3.1.4
[97] tweenr_1.0.2 stringi_1.7.4 ps_1.6.0 desc_1.3.0
[101] lattice_0.20-44 Matrix_1.3-4 vctrs_0.3.8 pillar_1.6.2
[105] lifecycle_1.0.0 spatstat.geom_2.2-2 lmtest_0.9-38 RcppAnnoy_0.0.19
[109] data.table_1.14.0 cowplot_1.1.1 bitops_1.0-7 irlba_2.3.3
[113] httpuv_1.6.3 patchwork_1.1.1 R6_2.5.1 promises_1.2.0.1
[117] lsa_0.73.2 KernSmooth_2.23-20 gridExtra_2.3 parallelly_1.28.1
[121] sessioninfo_1.1.1 codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1
[125] pkgload_1.2.2 rprojroot_2.0.2 withr_2.4.2 SeuratObject_4.0.2
[129] qlcMatrix_0.9.7 sctransform_0.3.2 Rsamtools_2.8.0 GenomeInfoDbData_1.2.6
[133] mgcv_1.8-36 grid_4.1.1 rpart_4.1-15 tidyr_1.1.3
[137] Rtsne_0.15 ggforce_0.3.3 shiny_1.7.0
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