Calculate clone fate bias for specific cell type
clone_fate_bias.RdCalculate clone fate bias for specific cell type
Arguments
- data
data.frame, indicating lineage tracing data, first column should be lineage tracing barcodes, second column should be related cell type
- fate_use
character, targeted fate cell type. if fate_use == '', this function will automatically select clone dominant cell type.
Examples
clone_fate_bias(fate_test)
#> [1] "stromal cell"
#> clone_name fate_use clone_size fate_ratio
#> I I stromal cell 12 0.0833333333333333
#> X1 1 stromal cell 32 0.59375
#> X9 9 stromal cell 66 0.484848484848485
#> X123 123 stromal cell 27 0.592592592592593
#> X1234789 1234789 stromal cell 2 1
#> X56IHG 56IHG stromal cell 2 1
#> C C stromal cell 5 0.2
#> X56789 56789 stromal cell 5 0.2
#> X3FE 3FE stromal cell 1 1
#> IFE IFE stromal cell 1 1
#> X12G 12G stromal cell 1 1
#> X145 145 stromal cell 1 1
#> X1256789 1256789 stromal cell 1 1
#> X12347 12347 stromal cell 1 1
#> X123456789 123456789 stromal cell 1 1
#> X12C69 12C69 stromal cell 1 1
#> X12GFEDC89 12GFEDC89 stromal cell 1 1
#> CB14GFE CB14GFE stromal cell 1 1
#> EDA EDA stromal cell 1 1
#> X7H9 7H9 stromal cell 1 1
#> CB56789 CB56789 stromal cell 1 1
#> CBAHG CBAHG stromal cell 1 1
#> X1HEDCB9 1HEDCB9 stromal cell 1 1
#> X12345F9 12345F9 stromal cell 1 1
#> C456IHG C456IHG stromal cell 1 1
#> X16G 16G stromal cell 1 1
#> X125 125 stromal cell 1 1
#> X123FED9 123FED9 stromal cell 1 1
#> X12589 12589 stromal cell 1 1
#> X3456789 3456789 stromal cell 1 1
#> X589 589 stromal cell 1 1
#> X12789 12789 stromal cell 1 1
#> X14589 14589 stromal cell 1 1
#> X12E 12E stromal cell 1 1
#> AD5 AD5 stromal cell 1 1
#> X567H9 567H9 stromal cell 1 1
#> X5HGBA 5HGBA stromal cell 1 1
#> X1234589 1234589 stromal cell 1 1
#> X16I8G 16I8G stromal cell 1 1
#> X14IHGFE 14IHGFE stromal cell 1 1
#> A2349 A2349 stromal cell 1 1
#> CBA4IHG CBA4IHG stromal cell 1 1
#> X129 129 stromal cell 22 0.363636363636364
#> X189 189 stromal cell 12 0.333333333333333
#> IFC IFC stromal cell 3 0.666666666666667
#> X1234569 1234569 stromal cell 4 0.25
#> X7 7 stromal cell 5 0.6
#> GFC GFC stromal cell 5 0.6
#> X149 149 stromal cell 6 0.333333333333333
#> X3 3 stromal cell 23 0.478260869565217
#> X5 5 stromal cell 3 0.333333333333333
#> X789 789 stromal cell 5 0.4
#> X16I 16I stromal cell 3 0.333333333333333
#> X14789 14789 stromal cell 2 0.5
#> X12345 12345 stromal cell 3 0.333333333333333
#> C81 C81 stromal cell 4 0.5
#> X569 569 stromal cell 3 0.333333333333333
#> E E stromal cell 2 0.5
#> X749 749 stromal cell 2 0.5
#> X12349 12349 stromal cell 9 0.444444444444444
#> A23 A23 stromal cell 3 0.333333333333333
#> CB9 CB9 stromal cell 3 0.333333333333333
#> X3D9 3D9 stromal cell 2 0.5
#> X12389 12389 stromal cell 3 0.333333333333333
#> pvalue fdr
#> I 0.0145160768151399 0.0145160768151399
#> X1 0.0608235969466868 0.0608235969466868
#> X9 0.0995901067413939 0.0995901067413939
#> X123 0.105983669882209 0.105983669882209
#> X1234789 0.214555812830038 0.214555812830038
#> X56IHG 0.214555812830038 0.214555812830038
#> C 0.379469229242591 0.379469229242591
#> X56789 0.379469229242591 0.379469229242591
#> X3FE 0.465317919075145 0.465317919075145
#> IFE 0.465317919075145 0.465317919075145
#> X12G 0.465317919075145 0.465317919075145
#> X145 0.465317919075145 0.465317919075145
#> X1256789 0.465317919075145 0.465317919075145
#> X12347 0.465317919075145 0.465317919075145
#> X123456789 0.465317919075145 0.465317919075145
#> X12C69 0.465317919075145 0.465317919075145
#> X12GFEDC89 0.465317919075145 0.465317919075145
#> CB14GFE 0.465317919075145 0.465317919075145
#> EDA 0.465317919075145 0.465317919075145
#> X7H9 0.465317919075145 0.465317919075145
#> CB56789 0.465317919075145 0.465317919075145
#> CBAHG 0.465317919075145 0.465317919075145
#> X1HEDCB9 0.465317919075145 0.465317919075145
#> X12345F9 0.465317919075145 0.465317919075145
#> C456IHG 0.465317919075145 0.465317919075145
#> X16G 0.465317919075145 0.465317919075145
#> X125 0.465317919075145 0.465317919075145
#> X123FED9 0.465317919075145 0.465317919075145
#> X12589 0.465317919075145 0.465317919075145
#> X3456789 0.465317919075145 0.465317919075145
#> X589 0.465317919075145 0.465317919075145
#> X12789 0.465317919075145 0.465317919075145
#> X14589 0.465317919075145 0.465317919075145
#> X12E 0.465317919075145 0.465317919075145
#> AD5 0.465317919075145 0.465317919075145
#> X567H9 0.465317919075145 0.465317919075145
#> X5HGBA 0.465317919075145 0.465317919075145
#> X1234589 0.465317919075145 0.465317919075145
#> X16I8G 0.465317919075145 0.465317919075145
#> X14IHGFE 0.465317919075145 0.465317919075145
#> A2349 0.465317919075145 0.465317919075145
#> CBA4IHG 0.465317919075145 0.465317919075145
#> X129 0.513439912481979 0.513439912481979
#> X189 0.558124870810537 0.558124870810537
#> IFC 0.597915933089743 0.597915933089743
#> X1234569 0.627362703495069 0.627362703495069
#> X7 0.664626433145562 0.664626433145562
#> GFC 0.664626433145562 0.664626433145562
#> X149 0.691282799193364 0.691282799193364
#> X3 0.828687570264039 0.828687570264039
#> X5 1 1
#> X789 1 1
#> X16I 1 1
#> X14789 1 1
#> X12345 1 1
#> C81 1 1
#> X569 1 1
#> E 1 1
#> X749 1 1
#> X12349 1 1
#> A23 1 1
#> CB9 1 1
#> X3D9 1 1
#> X12389 1 1