jiang-junyao / cacimar Goto Github PK

How can I generate multiple species' .rda files like zf_mm_ch_markers.rda using my data ? The tutorial does not cover this, please tell me

I tried to run the Identify_Markers command, but the following error has occurred.

hs_marker <- Identify_Markers(my_object,PowerCutoff=0.35, DifferenceCutoff=0.1)
Calculating cluster 0
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 39s
Calculating cluster 1
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 03s
Calculating cluster 2
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 20s
Calculating cluster 3
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 23s
Calculating cluster 4
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=50s
Calculating cluster 5
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 28s
Calculating cluster 6
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=45s
Calculating cluster 7
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 21s
Calculating cluster 8
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 25s
Calculating cluster 9
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 16s
Calculating cluster 10
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 19s
Calculating cluster 11
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02m 20s
Calculating cluster 12
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 06s
Calculating cluster 13
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=27s
Calculating cluster 14
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 58s
[1] "0"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 09s
[1] "1"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 11s
[1] "2"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 12s
[1] "3"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 20s
[1] "4"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 16s
[1] "5"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 21s
[1] "6"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 07s
[1] "7"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 04s
[1] "8"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 03s
[1] "9"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 02s
[1] "10"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 06s
[1] "11"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 06s
[1] "12"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 05s
[1] "13"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 04s
[1] "14"
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06m 02s
[1] "0" "0" "15986"
[1] "1" "0" "10727"
[1] "2" "0" "8098"
[1] "3" "0" "5973"
[1] "4" "0" "5939"
[1] "5" "0" "5795"
[1] "6" "0" "5487"
[1] "7" "0" "5480"
[1] "8" "0" "3961"
[1] "9" "0" "2793"
[1] "10" "0" "2383"
[1] "11" "0" "1631"
[1] "12" "0" "620"
[1] "13" "0" "366"
[1] "14" "0" "335"
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 833, 2000

My seurat object was created with Seurat v4.4.0 (R 4.2.0). The result with Seurat v5 (R 4.3.3) was the same as this.

When I follow the tutorial and run the code. There was an error
conserved_markers = identify_conserved_marker(OrthG_Mm_Zf,marker_spec1, marker_spec2,

•                                           Species_name1 = 'mm',
  

•                                           Species_name2 = 'zf',conserved_celltype_pair = conserved_celltype)
  

Error in if (class(conserved_gene) == "matrix") { :
the condition has length > 1

In the Identify_ConservedCellTypes step, the following error occurred.

OrthG <- OrthG_Hs_Mm
expression <- Identify_ConservedCellTypes(OrthG, mm_marker, hs_marker, 'mm', 'hs')

Error in Identify_ConservedCellTypes(OrthG, mm_marker, hs_marker, "mm", :
Species1_Marker_table should contain power column!

My mm_marker object is as follows:

head (mm_marker object)
AllCluster Allpower NumCluster Cluster Pvalue Cluster0
0610010K14Rik Cluster11,Cluster4 0.35,0.252 2 Cluster11 3.074129e-05 0.47692308
1110002L01Rik Cluster22,Cluster21 0.42,0.18 2 Cluster22 1.534010e-03 0.03426573
1110046J04Rik Cluster22,Cluster18 0.488,0.226 2 Cluster22 2.510126e-06 0.05524476
1110051M20Rik Cluster22,Cluster8 0.444,0.294 2 Cluster22 1.640159e-04 0.09300699
1110065P20Rik Cluster22,Cluster18 0.41,0.268 2 Cluster22 9.964978e-06 0.31678322
1190005I06Rik Cluster23,Cluster24,Cluster19 0.386,0.248,0.0800000000000001 3 Cluster23 6.613419e-03 0.03916084
Cluster1 Cluster2 Cluster3 Cluster4 Cluster5 Cluster6 Cluster7 Cluster8 Cluster9 Cluster10
0610010K14Rik 0.44271239 0.32967033 0.59689922 0.8977273 0.74849579 0.6194444 0.65997131 0.82395382 0.71304348 0.58904110
1110002L01Rik 0.03897116 0.04029304 0.07364341 0.1931818 0.15282792 0.1111111 0.07890961 0.15151515 0.20724638 0.06240487
1110046J04Rik 0.08963367 0.05860806 0.25387597 0.3615702 0.29121540 0.2125000 0.16642755 0.25685426 0.31159420 0.11263318
1110051M20Rik 0.10756041 0.08699634 0.27519380 0.5165289 0.45367028 0.2555556 0.18507891 0.53679654 0.41014493 0.16438356
1110065P20Rik 0.32579891 0.21062271 0.43217054 0.7438017 0.64741276 0.4486111 0.49784792 0.69408369 0.62028986 0.43378995
1190005I06Rik 0.04598597 0.02838828 0.03003876 0.1022727 0.08423586 0.0500000 0.08034433 0.08946609 0.06956522 0.05327245
Cluster11 Cluster12 Cluster13 Cluster14 Cluster15 Cluster16 Cluster17 Cluster18 Cluster19 Cluster20
0610010K14Rik 0.84509202 0.45679012 0.42723881 0.69030733 0.79259259 0.82644628 0.75714286 0.8305648 0.8861386 0.37974684
1110002L01Rik 0.10736196 0.04475309 0.02611940 0.07092199 0.26913580 0.17630854 0.18000000 0.2059801 0.1237624 0.08860759
1110046J04Rik 0.20552147 0.06944444 0.03358209 0.09219858 0.35555556 0.39393939 0.36857143 0.4219269 0.3069307 0.13924051
1110051M20Rik 0.30674847 0.07716049 0.08955224 0.20803783 0.46419753 0.47382920 0.47428571 0.5614618 0.3415842 0.13924051
1110065P20Rik 0.57515337 0.31172840 0.21455224 0.41607565 0.61728395 0.75482094 0.63428571 0.7607973 0.6732673 0.40506329
1190005I06Rik 0.07515337 0.03858025 0.01679104 0.02127660 0.09135802 0.05785124 0.08857143 0.0897010 0.1435644 0.03797468
Cluster21 Cluster22 Cluster23 Cluster24
0610010K14Rik 0.7662338 1.0000000 0.68115942 0.34482759
1110002L01Rik 0.2857143 0.5571429 0.07246377 0.06896552
1110046J04Rik 0.1818182 0.7428571 0.17391304 0.08620690
1110051M20Rik 0.4415584 0.8142857 0.31884058 0.17241379
1110065P20Rik 0.6623377 0.9714286 0.50724638 0.62068966
1190005I06Rik 0.1038961 0.1428571 0.43478261 0.31034483

It would be helpful if there are any suggestions about it.

同源基因数据库是否只有斑马鱼小鼠等这十个物种，我想测试猪和人的同源性是否能使用其他同源基因数据库代替呢？
辛苦啦

I am opening this issue as a notification because CACIMAR is listed here as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5 as a beta in March of this year, with new updates for spatial, multimodal, and massively scalable analysis. For more information on updates and improvements, check out our website https://satijalab.org/seurat/.
We are now preparing to release Seurat v5 to CRAN, and plan to submit it on October 23rd. While we have tried our best to keep things backward-compatible, it is possible that updates to Seurat and SeuratObject might break your existing functionality or tests. We wanted to reach out before the new version is on CRAN, so that there's time to report issues/incompatibilities and prepare you for any changes in your code base that might be necessary.

We apologize for any disruption or inconvenience, but hope that the improvements to Seurat v5 will benefit your users going forward.
To test the upcoming release, you can install Seurat from the seurat5 branch using the instructions available on this page: https://satijalab.org/seurat/articles/install.

Thank you!
Seurat v5 team

Hi, sorry to bother you again. This time, when I runing build homologous gene database function for macaque and mouse, the following error occurred.

Species_name1 <- 'rh'
Species_name2 <- 'mm'
OrthG_Rh_Mm <- buildHomDatabase(HOM,Species_name1,Species_name2)

**Error in order(Sp1$HomoloGene.ID) : argument 1 is not a vector**

And I found the same error with the sample data. I think the problem may be that there is no HomoloGene.ID column in the MGI database.
If you could help I would really appreciate it.
Thanks