tests/testthat/_snaps/mageck_rra.md
In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses
MageckGeneRRA filter returns results
Code
get_mageck_gene_summary(test_gene_summary_obj, filters = "neg.fdr < 0.05")
Output
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 NEG1 9 7.1884e-13 2.6873e-07 6.6e-05 1 9 -2.7520
2 NEG2 5 4.9934e-12 2.6873e-07 6.6e-05 2 5 -2.7056
3 NEG3 5 1.3418e-11 2.6873e-07 6.6e-05 3 5 -3.7000
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 1 1 1 18422 0 -2.7520
2 1 1 1 18421 0 -2.7056
3 1 1 1 18420 0 -3.7000
read MAGeCK RRA gene summary
Code
test_gene_summary_obj
Output
An object of class "MageckGeneRRA"
Slot "filepath":
[1] "test"
Slot "gene_summary":
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 NEG1 9 7.1884e-13 2.6873e-07 0.000066 1 9 -2.7520
2 NEG2 5 4.9934e-12 2.6873e-07 0.000066 2 5 -2.7056
3 NEG3 5 1.3418e-11 2.6873e-07 0.000066 3 5 -3.7000
4 NONSIG1 5 3.2729e-06 1.4243e-03 0.105000 239 5 -1.4231
5 NONSIG2 5 3.2846e-06 1.4243e-03 0.105000 240 4 -1.9873
6 NONSIG3 5 3.3205e-06 1.4243e-03 0.105000 241 5 -2.3140
7 POS3 5 1.0000e+00 1.0000e+00 1.000000 18420 0 1.1215
8 POS2 5 1.0000e+00 1.0000e+00 1.000000 18421 0 1.2517
9 POS1 5 1.0000e+00 1.0000e+00 1.000000 18422 0 1.2391
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 1.0000e+00 1.0000e+00 1.000000 18422 0 -2.7520
2 1.0000e+00 1.0000e+00 1.000000 18421 0 -2.7056
3 1.0000e+00 1.0000e+00 1.000000 18420 0 -3.7000
4 1.0000e+00 9.9999e-01 1.000000 18214 0 -1.4231
5 9.7746e-01 9.7759e-01 1.000000 16700 0 -1.9873
6 9.9998e-01 9.9998e-01 1.000000 18093 0 -2.3100
7 1.0721e-08 2.6873e-07 0.000309 9 5 1.1215
8 3.2063e-09 2.6873e-07 0.000309 5 5 1.2517
9 2.0448e-10 2.6873e-07 0.000309 2 5 1.2391
MageckSgrnaRRA filter returns results
Code
get_mageck_sgrna_summary(test_sgrna_summary_obj, filters = "FDR < 0.05")
Output
sgrna Gene control_count treatment_count control_mean treat_mean
1 sgRNA1 NEG1 142.690 961.11/850.43/454.83 142.690 850.43000
2 sgRNA2 NEG1 90.208 630.66/592.44/243.95 90.208 592.44000
3 sgRNA3 NEG1 167.950 792.56/323.78/1074.7 167.950 792.56000
4 sgRNA4 gene2 535.670 135.08/105.16/90.989 535.670 105.16000
5 sgRNA5 gene2 187.630 34.896/4.6038/3.3691 187.630 4.60380
6 sgRNA6 gene2 87.091 0.33972/0.33972/4.9179 87.091 0.33972
LFC control_var adj_var score p.low p.high p.twosided
1 2.5669 84374.00 1915.10 16.1730 1.0000e+00 3.9430e-59 7.8860e-59
2 2.7019 61451.00 1044.60 15.5390 1.0000e+00 9.4344e-55 1.8869e-54
3 2.2317 149670.00 2376.50 12.8120 1.0000e+00 6.9816e-38 1.3963e-37
4 -2.3377 548.00 11106.00 4.0870 2.1849e-05 9.9998e-01 4.3697e-05
5 -5.0730 459.58 2752.60 3.8132 6.8588e-05 9.9993e-01 1.3718e-04
6 -6.0390 10.48 997.24 3.7256 9.7440e-05 9.9990e-01 1.9488e-04
FDR high_in_treatment
1 7.0296e-54 True
2 8.4099e-50 True
3 4.1489e-33 True
4 6.4597e-03 False
5 1.4613e-02 False
6 1.9111e-02 False
read MAGeCK RRA sgRNA summary
Code
test_sgrna_summary_obj
Output
An object of class "MageckSgrnaRRA"
Slot "filepath":
[1] "test"
Slot "sgrna_summary":
sgrna Gene control_count treatment_count control_mean treat_mean
1 sgRNA1 NEG1 142.690 961.11/850.43/454.83 142.690 850.43000
2 sgRNA2 NEG1 90.208 630.66/592.44/243.95 90.208 592.44000
3 sgRNA3 NEG1 167.950 792.56/323.78/1074.7 167.950 792.56000
4 sgRNA4 gene2 535.670 135.08/105.16/90.989 535.670 105.16000
5 sgRNA5 gene2 187.630 34.896/4.6038/3.3691 187.630 4.60380
6 sgRNA6 gene2 87.091 0.33972/0.33972/4.9179 87.091 0.33972
7 sgRNA7 gene3 105.950 221.97/94.709/219.35 105.950 219.35000
8 sgRNA8 gene4 143.680 377.05/282.36/266.08 143.680 282.36000
9 sgRNA9 gene4 113.010 231.32/177.98/231.7 113.010 231.32000
10 sgRNA10 gene5 86.927 16.801/2.53/1.0429 86.927 2.53000
11 sgRNA11 gene5 183.530 62.401/7.7788/23.724 183.530 23.72400
12 sgRNA12 gene5 208.300 33.177/18.574/43.939 208.300 33.17700
LFC control_var adj_var score p.low p.high p.twosided
1 2.5669 84374.00 1915.10 16.1730 1.0000e+00 3.9430e-59 7.8860e-59
2 2.7019 61451.00 1044.60 15.5390 1.0000e+00 9.4344e-55 1.8869e-54
3 2.2317 149670.00 2376.50 12.8120 1.0000e+00 6.9816e-38 1.3963e-37
4 -2.3377 548.00 11106.00 4.0870 2.1849e-05 9.9998e-01 4.3697e-05
5 -5.0730 459.58 2752.60 3.8132 6.8588e-05 9.9993e-01 1.3718e-04
6 -6.0390 10.48 997.24 3.7256 9.7440e-05 9.9990e-01 1.9488e-04
7 1.0428 7771.20 1291.80 3.1550 9.9920e-01 8.0378e-04 1.6076e-03
8 0.9698 4615.40 1932.60 3.1546 9.9920e-01 8.0396e-04 1.6079e-03
9 1.0270 1422.40 1406.70 3.1545 9.9920e-01 8.0496e-04 1.6099e-03
10 -4.6386 102.94 994.76 3.1544 8.0419e-04 9.9920e-01 1.6084e-03
11 -2.8999 875.06 2673.10 3.1541 8.0510e-04 9.9919e-01 1.6102e-03
12 -2.6144 164.54 3161.80 3.1502 8.1586e-04 9.9918e-01 1.6317e-03
FDR high_in_treatment
1 7.0296e-54 True
2 8.4099e-50 True
3 4.1489e-33 True
4 6.4597e-03 False
5 1.4613e-02 False
6 1.9111e-02 False
7 7.8177e-02 True
8 7.8177e-02 True
9 7.8177e-02 True
10 7.8177e-02 False
11 7.8177e-02 False
12 7.8844e-02 False
get MAGeCK RRA sgRNA summary per gene
Code
get_mageck_sgrna_gene_results(object = test_sgrna_summary_obj, gene = "NEG1")
Output
sgrna Gene control_count treatment_count control_mean treat_mean LFC
1 sgRNA1 NEG1 142.690 961.11/850.43/454.83 142.690 850.43 2.5669
2 sgRNA2 NEG1 90.208 630.66/592.44/243.95 90.208 592.44 2.7019
3 sgRNA3 NEG1 167.950 792.56/323.78/1074.7 167.950 792.56 2.2317
control_var adj_var score p.low p.high p.twosided FDR
1 84374 1915.1 16.173 1 3.9430e-59 7.8860e-59 7.0296e-54
2 61451 1044.6 15.539 1 9.4344e-55 1.8869e-54 8.4099e-50
3 149670 2376.5 12.812 1 6.9816e-38 1.3963e-37 4.1489e-33
high_in_treatment
1 True
2 True
3 True
can get top n depleted genes from MAGeCK RRA gene summary
Code
gene_summary_top_n_genes(gene_summary_object = test_gene_summary_obj, n = 3)
Output
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 NEG1 9 7.1884e-13 2.6873e-07 6.6e-05 1 9 -2.7520
2 NEG2 5 4.9934e-12 2.6873e-07 6.6e-05 2 5 -2.7056
3 NEG3 5 1.3418e-11 2.6873e-07 6.6e-05 3 5 -3.7000
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 1 1 1 18422 0 -2.7520
2 1 1 1 18421 0 -2.7056
3 1 1 1 18420 0 -3.7000
can get top n enriched genes from MAGeCK RRA gene summary
Code
gene_summary_top_n_genes(gene_summary_object = test_gene_summary_obj,
direction = "pos", n = 3)
Warning <simpleWarning>
Fewer than n top genes returned:1
Output
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 POS1 5 1 1 1 18422 0 1.2391
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 2.0448e-10 2.6873e-07 0.000309 2 5 1.2391
cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.
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MageckGeneRRA filter returns results
Code
get_mageck_gene_summary(test_gene_summary_obj, filters = "neg.fdr < 0.05")
Output
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 NEG1 9 7.1884e-13 2.6873e-07 6.6e-05 1 9 -2.7520
2 NEG2 5 4.9934e-12 2.6873e-07 6.6e-05 2 5 -2.7056
3 NEG3 5 1.3418e-11 2.6873e-07 6.6e-05 3 5 -3.7000
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 1 1 1 18422 0 -2.7520
2 1 1 1 18421 0 -2.7056
3 1 1 1 18420 0 -3.7000
read MAGeCK RRA gene summary
Code
test_gene_summary_obj
Output
An object of class "MageckGeneRRA"
Slot "filepath":
[1] "test"
Slot "gene_summary":
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 NEG1 9 7.1884e-13 2.6873e-07 0.000066 1 9 -2.7520
2 NEG2 5 4.9934e-12 2.6873e-07 0.000066 2 5 -2.7056
3 NEG3 5 1.3418e-11 2.6873e-07 0.000066 3 5 -3.7000
4 NONSIG1 5 3.2729e-06 1.4243e-03 0.105000 239 5 -1.4231
5 NONSIG2 5 3.2846e-06 1.4243e-03 0.105000 240 4 -1.9873
6 NONSIG3 5 3.3205e-06 1.4243e-03 0.105000 241 5 -2.3140
7 POS3 5 1.0000e+00 1.0000e+00 1.000000 18420 0 1.1215
8 POS2 5 1.0000e+00 1.0000e+00 1.000000 18421 0 1.2517
9 POS1 5 1.0000e+00 1.0000e+00 1.000000 18422 0 1.2391
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 1.0000e+00 1.0000e+00 1.000000 18422 0 -2.7520
2 1.0000e+00 1.0000e+00 1.000000 18421 0 -2.7056
3 1.0000e+00 1.0000e+00 1.000000 18420 0 -3.7000
4 1.0000e+00 9.9999e-01 1.000000 18214 0 -1.4231
5 9.7746e-01 9.7759e-01 1.000000 16700 0 -1.9873
6 9.9998e-01 9.9998e-01 1.000000 18093 0 -2.3100
7 1.0721e-08 2.6873e-07 0.000309 9 5 1.1215
8 3.2063e-09 2.6873e-07 0.000309 5 5 1.2517
9 2.0448e-10 2.6873e-07 0.000309 2 5 1.2391
MageckSgrnaRRA filter returns results
Code
get_mageck_sgrna_summary(test_sgrna_summary_obj, filters = "FDR < 0.05")
Output
sgrna Gene control_count treatment_count control_mean treat_mean
1 sgRNA1 NEG1 142.690 961.11/850.43/454.83 142.690 850.43000
2 sgRNA2 NEG1 90.208 630.66/592.44/243.95 90.208 592.44000
3 sgRNA3 NEG1 167.950 792.56/323.78/1074.7 167.950 792.56000
4 sgRNA4 gene2 535.670 135.08/105.16/90.989 535.670 105.16000
5 sgRNA5 gene2 187.630 34.896/4.6038/3.3691 187.630 4.60380
6 sgRNA6 gene2 87.091 0.33972/0.33972/4.9179 87.091 0.33972
LFC control_var adj_var score p.low p.high p.twosided
1 2.5669 84374.00 1915.10 16.1730 1.0000e+00 3.9430e-59 7.8860e-59
2 2.7019 61451.00 1044.60 15.5390 1.0000e+00 9.4344e-55 1.8869e-54
3 2.2317 149670.00 2376.50 12.8120 1.0000e+00 6.9816e-38 1.3963e-37
4 -2.3377 548.00 11106.00 4.0870 2.1849e-05 9.9998e-01 4.3697e-05
5 -5.0730 459.58 2752.60 3.8132 6.8588e-05 9.9993e-01 1.3718e-04
6 -6.0390 10.48 997.24 3.7256 9.7440e-05 9.9990e-01 1.9488e-04
FDR high_in_treatment
1 7.0296e-54 True
2 8.4099e-50 True
3 4.1489e-33 True
4 6.4597e-03 False
5 1.4613e-02 False
6 1.9111e-02 False
read MAGeCK RRA sgRNA summary
Code
test_sgrna_summary_obj
Output
An object of class "MageckSgrnaRRA"
Slot "filepath":
[1] "test"
Slot "sgrna_summary":
sgrna Gene control_count treatment_count control_mean treat_mean
1 sgRNA1 NEG1 142.690 961.11/850.43/454.83 142.690 850.43000
2 sgRNA2 NEG1 90.208 630.66/592.44/243.95 90.208 592.44000
3 sgRNA3 NEG1 167.950 792.56/323.78/1074.7 167.950 792.56000
4 sgRNA4 gene2 535.670 135.08/105.16/90.989 535.670 105.16000
5 sgRNA5 gene2 187.630 34.896/4.6038/3.3691 187.630 4.60380
6 sgRNA6 gene2 87.091 0.33972/0.33972/4.9179 87.091 0.33972
7 sgRNA7 gene3 105.950 221.97/94.709/219.35 105.950 219.35000
8 sgRNA8 gene4 143.680 377.05/282.36/266.08 143.680 282.36000
9 sgRNA9 gene4 113.010 231.32/177.98/231.7 113.010 231.32000
10 sgRNA10 gene5 86.927 16.801/2.53/1.0429 86.927 2.53000
11 sgRNA11 gene5 183.530 62.401/7.7788/23.724 183.530 23.72400
12 sgRNA12 gene5 208.300 33.177/18.574/43.939 208.300 33.17700
LFC control_var adj_var score p.low p.high p.twosided
1 2.5669 84374.00 1915.10 16.1730 1.0000e+00 3.9430e-59 7.8860e-59
2 2.7019 61451.00 1044.60 15.5390 1.0000e+00 9.4344e-55 1.8869e-54
3 2.2317 149670.00 2376.50 12.8120 1.0000e+00 6.9816e-38 1.3963e-37
4 -2.3377 548.00 11106.00 4.0870 2.1849e-05 9.9998e-01 4.3697e-05
5 -5.0730 459.58 2752.60 3.8132 6.8588e-05 9.9993e-01 1.3718e-04
6 -6.0390 10.48 997.24 3.7256 9.7440e-05 9.9990e-01 1.9488e-04
7 1.0428 7771.20 1291.80 3.1550 9.9920e-01 8.0378e-04 1.6076e-03
8 0.9698 4615.40 1932.60 3.1546 9.9920e-01 8.0396e-04 1.6079e-03
9 1.0270 1422.40 1406.70 3.1545 9.9920e-01 8.0496e-04 1.6099e-03
10 -4.6386 102.94 994.76 3.1544 8.0419e-04 9.9920e-01 1.6084e-03
11 -2.8999 875.06 2673.10 3.1541 8.0510e-04 9.9919e-01 1.6102e-03
12 -2.6144 164.54 3161.80 3.1502 8.1586e-04 9.9918e-01 1.6317e-03
FDR high_in_treatment
1 7.0296e-54 True
2 8.4099e-50 True
3 4.1489e-33 True
4 6.4597e-03 False
5 1.4613e-02 False
6 1.9111e-02 False
7 7.8177e-02 True
8 7.8177e-02 True
9 7.8177e-02 True
10 7.8177e-02 False
11 7.8177e-02 False
12 7.8844e-02 False
get MAGeCK RRA sgRNA summary per gene
Code
get_mageck_sgrna_gene_results(object = test_sgrna_summary_obj, gene = "NEG1")
Output
sgrna Gene control_count treatment_count control_mean treat_mean LFC
1 sgRNA1 NEG1 142.690 961.11/850.43/454.83 142.690 850.43 2.5669
2 sgRNA2 NEG1 90.208 630.66/592.44/243.95 90.208 592.44 2.7019
3 sgRNA3 NEG1 167.950 792.56/323.78/1074.7 167.950 792.56 2.2317
control_var adj_var score p.low p.high p.twosided FDR
1 84374 1915.1 16.173 1 3.9430e-59 7.8860e-59 7.0296e-54
2 61451 1044.6 15.539 1 9.4344e-55 1.8869e-54 8.4099e-50
3 149670 2376.5 12.812 1 6.9816e-38 1.3963e-37 4.1489e-33
high_in_treatment
1 True
2 True
3 True
can get top n depleted genes from MAGeCK RRA gene summary
Code
gene_summary_top_n_genes(gene_summary_object = test_gene_summary_obj, n = 3)
Output
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 NEG1 9 7.1884e-13 2.6873e-07 6.6e-05 1 9 -2.7520
2 NEG2 5 4.9934e-12 2.6873e-07 6.6e-05 2 5 -2.7056
3 NEG3 5 1.3418e-11 2.6873e-07 6.6e-05 3 5 -3.7000
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 1 1 1 18422 0 -2.7520
2 1 1 1 18421 0 -2.7056
3 1 1 1 18420 0 -3.7000
can get top n enriched genes from MAGeCK RRA gene summary
Code
gene_summary_top_n_genes(gene_summary_object = test_gene_summary_obj,
direction = "pos", n = 3)
Warning <simpleWarning>
Fewer than n top genes returned:1
Output
id num neg.score neg.p.value neg.fdr neg.rank neg.goodsgrna neg.lfc
1 POS1 5 1 1 1 18422 0 1.2391
pos.score pos.p.value pos.fdr pos.rank pos.goodsgrna pos.lfc
1 2.0448e-10 2.6873e-07 0.000309 2 5 1.2391
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