An issue in addGeneIntegrationMatrix

[Fugwaaaa]

When i use the addGeneIntegrationMatrix function to integrate the ATAC-data and scRNA-data, and gain the GeneIntegrationMatrix,. But there are only 21561 overlapping genes corresponds from gene scores and rna matrix. And there is a very important gene that is not included among these 21561 genes. Is there any way to solve this problem?

projlung.Epi2 <- addGeneIntegrationMatrix(

• ArchRProj = projlung.Epi2,
• useMatrix = "GeneScoreMatrix",
• matrixName = "GeneIntegrationMatrix_epi",
• reducedDims = "Harmony_epi",
• seRNA = subsc,
• addToArrow = TRUE,#这样才能有GeneIntegrationMatrix
• force= TRUE,
• dimsToUse = 1:100,
• corCutOff = 0.75,
• groupRNA = "Celltype7",
• nameCell = "predictedCell_Un",
• nameGroup = "predictedGroup_Un",
• nameScore = "predictedScore_Un"
• )
  ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-3b30f931527119-Date-2025-08-22_Time-09-22-13.945094.log
  If there is an issue, please report to github with logFile!
  2025-08-22 09:22:14.781708 : Running Seurat's Integration Stuart* et al 2019, 0.014 mins elapsed.
  2025-08-22 09:22:14.814906 : Checking ATAC Input, 0.014 mins elapsed.
  2025-08-22 09:22:15.834434 : Checking RNA Input, 0.031 mins elapsed.
  2025-08-22 09:22:22.611854 : Found 21561 overlapping gene names from gene scores and rna matrix!, 0.144 mins elapsed.
  2025-08-22 09:22:22.61335 : Creating Integration Blocks, 0.144 mins elapsed.
  2025-08-22 09:22:22.82761 : Prepping Interation Data, 0.148 mins elapsed.
  Disabling H5 File Locking. If this is not desired check addArchRLocking.
  subThreading Enabled since ArchRLocking is FALSE see addArchRLocking
  Warning! Not all requested dimsToUse are available! The follow dims were not found in Harmony_epi:
  31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100
  Unavailable dims will be automatically excluded...
  2025-08-22 09:22:24.284907 : Computing Integration in 1 Integration Blocks!, 0 mins elapsed.
  2025-08-22 09:22:24.293454 : Block (1 of 1) : Computing Integration, 0 mins elapsed.
  2025-08-22 09:22:32.991569 : Block (1 of 1) : Identifying Variable Genes, 0.145 mins elapsed.
  警告: Different features in new layer data than already exists for scale.data
  2025-08-22 09:22:36.437615 : Block (1 of 1) : Getting GeneScoreMatrix, 0.203 mins elapsed.
  2025-08-22 09:22:41.381823 : Block (1 of 1) : Imputing GeneScoreMatrix, 0.285 mins elapsed.
  Getting ImputeWeights
  2025-08-22 09:22:46.35352 : Block (1 of 1) : Seurat FindTransferAnchors, 0.368 mins elapsed.
  2025-08-22 09:23:53.529552 : Block (1 of 1) : Seurat TransferData Cell Group Labels, 1.487 mins elapsed.
  2025-08-22 09:23:54.602974 : Block (1 of 1) : Seurat TransferData Cell Names Labels, 1.505 mins elapsed.
  2025-08-22 09:23:59.612344 : Block (1 of 1) : Seurat TransferData GeneMatrix, 1.589 mins elapsed.
  2025-08-22 09:24:04.520037 : Block (1 of 1) : Saving TransferAnchors Joint CCA, 1.671 mins elapsed.
  2025-08-22 09:24:05.911217 : Block (1 of 1) : Transferring Paired RNA to Temp File, 1.694 mins elapsed.
  2025-08-22 09:24:08.576161 : Block (1 of 1) : Completed Integration, 1.738 mins elapsed.
  2025-08-22 09:24:09.783693 : Block (1 of 1) : Plotting Joint UMAP, 1.758 mins elapsed.
  2025-08-22 09:24:28.499282 : Transferring Data to ArrowFiles, 2.07 mins elapsed.
  2025-08-22 09:25:18.472618 : Completed Integration with RNA Matrix, 2.903 mins elapsed.
  Overriding previous entry for predictedCell_Un
  Overriding previous entry for predictedGroup_Un
  Overriding previous entry for predictedScore_Un
  ArchR logging successful to : ArchRLogs/ArchR-addGeneIntegrationMatrix-3b30f931527119-Date-2025-08-22_Time-09-22-13.945094.log
  警告信息:
  Key ‘rna_’ taken, using ‘sgokv_’ instead