Error in Identify_ConservedCellTypes

[stat-lab]

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.

[jiang-junyao]

Hi, could you send your 'mm_marker' and 'hs_marker' in csv or rds or txt format to me via email (jyjiang@link.cuhk.edu.hk)? Thanks.

[stat-lab]

I have now sent these files to you via email.
Thank you.

[Shiywa]

I got the same result like above files. Is there any updates for CACIMAR. the structure of output from Identify_Markers is not as same as the result in provided tutorial.

[Shiywa]

I got the same result like above files. Is there any updates for CACIMAR. the structure of output from Identify_Markers is not as same as the result in provided tutorial.

well, I guess I know what happened. the new result give genes' all powers in different cell types. I just need to filter and use the maxium power.

[jiang-junyao]

Hi, this problem occurs because the input format of your table is wrong. You can run the following codes to revise your table:
list_power_numeric <- lapply(strsplit(hs_marker$Allpower,','),
function(x) as.numeric(x))
max_values <- sapply(list_power_numeric, max)
hs_marker$power = max_values
hs_marker$cluster = hs_marker$Cluster
hs_marker$gene = rownames(hs_marker)

list_power_numeric <- lapply(strsplit(mm_marker$Allpower,','),
function(x) as.numeric(x))
max_values <- sapply(list_power_numeric, max)
mm_marker$power = max_values
mm_marker$cluster = mm_marker$Cluster
mm_marker$gene = rownames(mm_marker)

However, i have checked the codes of 'Identify_Markers' function. The function will automatically output the table in correct format. Maybe you can re-install the package to fix this problem.

Thanks!