get the the var_gene_list and topN (or top percent) most variable genes
Source:R/ngs_rnaseq.R
get_top_var_mat.Rdget the the var_gene_list and topN (or top percent) most variable genes
Value
a list of variance (var_genes_list) and the expression matrix of most-variable genes (topN_mat)
Examples
get_top_var_mat(count_df)
#> $var_genes
#> gene_1 gene_2 gene_3 gene_4 gene_5 gene_6 gene_7 gene_8
#> 103.67368 191.25000 135.83947 75.83947 72.48421 147.93684 119.08158 62.83158
#> gene_9 gene_10 gene_11 gene_12 gene_13 gene_14 gene_15 gene_16
#> 134.35789 109.41842 84.34474 101.35789 99.50263 74.46316 97.52368 97.92368
#> gene_17 gene_18 gene_19 gene_20 gene_21 gene_22 gene_23 gene_24
#> 79.62895 87.58947 154.80000 56.43158 106.04211 117.71316 107.18684 77.85263
#> gene_25 gene_26 gene_27 gene_28 gene_29 gene_30 gene_31 gene_32
#> 111.67368 41.94474 101.06316 70.13421 121.72632 89.46053 86.47368 121.73421
#> gene_33 gene_34 gene_35 gene_36 gene_37 gene_38 gene_39 gene_40
#> 48.66053 101.43158 78.21053 93.25000 116.68158 91.88421 173.88421 76.25263
#> gene_41 gene_42 gene_43 gene_44 gene_45 gene_46 gene_47 gene_48
#> 86.82895 104.83158 158.02895 145.31316 91.16842 64.97632 68.90526 68.25263
#> gene_49 gene_50 gene_51 gene_52 gene_53 gene_54 gene_55 gene_56
#> 137.62895 85.60789 125.85263 124.69474 72.51316 118.72632 92.62105 196.40789
#> gene_57 gene_58 gene_59 gene_60 gene_61 gene_62 gene_63 gene_64
#> 62.45000 74.93684 125.81842 118.23947 115.60789 75.67105 56.58947 63.41842
#> gene_65 gene_66 gene_67 gene_68 gene_69 gene_70 gene_71 gene_72
#> 89.22105 140.97632 88.58947 108.47105 75.31316 68.73684 103.83947 98.78684
#> gene_73 gene_74 gene_75 gene_76 gene_77 gene_78 gene_79 gene_80
#> 190.05000 115.14737 101.83947 94.57632 82.99737 63.18684 32.89211 69.98684
#> gene_81 gene_82 gene_83 gene_84 gene_85 gene_86 gene_87 gene_88
#> 86.15789 110.77895 124.25263 152.05000 70.76579 117.29211 145.29211 100.13421
#> gene_89 gene_90 gene_91 gene_92 gene_93 gene_94 gene_95 gene_96
#> 131.57895 76.55526 170.67368 82.19737 103.77895 105.05263 63.21053 103.06316
#> gene_97 gene_98 gene_99 gene_100
#> 77.85263 92.66053 57.72632 193.18684
#>
#> $topN_mat
#> sample_1 sample_2 sample_3 sample_4 sample_5 sample_6 sample_7
#> gene_56 115 100 111 81 90 84 103
#> gene_100 88 108 89 128 88 121 91
#> gene_2 104 111 98 109 109 122 121
#> gene_73 101 100 130 99 95 115 118
#> gene_39 123 95 129 97 91 93 91
#> gene_91 93 106 109 73 76 126 90
#> gene_43 75 109 102 85 97 93 94
#> gene_19 123 94 93 93 109 117 82
#> gene_84 124 101 110 106 92 122 94
#> gene_6 93 87 115 90 122 96 92
#> gene_44 96 87 98 89 99 109 92
#> gene_87 88 99 93 97 92 102 97
#> gene_66 101 123 124 113 105 103 85
#> gene_49 102 112 99 96 130 101 95
#> gene_3 102 111 90 109 118 114 101
#> gene_9 84 95 103 91 100 102 83
#> gene_89 101 96 102 79 88 87 103
#> gene_51 93 94 106 101 97 89 101
#> gene_59 99 111 117 93 102 93 104
#> gene_52 110 114 99 102 96 88 118
#> sample_8 sample_9 sample_10 sample_11 sample_12 sample_13 sample_14
#> gene_56 86 107 106 125 90 117 121
#> gene_100 100 105 69 96 85 99 87
#> gene_2 71 108 108 93 83 125 97
#> gene_73 99 91 110 94 108 95 120
#> gene_39 103 98 97 112 97 108 116
#> gene_91 117 91 99 92 100 96 95
#> gene_43 91 90 102 125 88 120 79
#> gene_19 96 108 117 109 116 106 120
#> gene_84 95 107 114 77 94 105 109
#> gene_6 104 111 99 100 104 126 95
#> gene_44 98 117 116 101 96 105 125
#> gene_87 117 99 105 93 102 91 106
#> gene_66 111 95 100 80 119 115 116
#> gene_49 99 124 93 87 89 103 84
#> gene_3 92 100 92 106 111 83 115
#> gene_9 99 103 111 112 129 93 97
#> gene_89 113 102 112 103 114 97 112
#> gene_51 103 101 90 108 131 107 74
#> gene_59 99 119 116 102 107 101 97
#> gene_52 88 101 103 80 105 87 110
#> sample_15 sample_16 sample_17 sample_18 sample_19 sample_20
#> gene_56 105 111 114 79 116 94
#> gene_100 101 111 89 111 108 109
#> gene_2 116 104 102 106 83 115
#> gene_73 100 97 118 72 114 83
#> gene_39 123 97 76 94 104 114
#> gene_91 83 98 108 103 87 110
#> gene_43 90 103 92 111 97 104
#> gene_19 99 95 78 100 111 110
#> gene_84 96 98 102 90 80 113
#> gene_6 122 107 109 85 89 102
#> gene_44 107 109 109 78 100 80
#> gene_87 111 87 77 102 134 95
#> gene_66 98 100 101 93 108 113
#> gene_49 95 101 109 113 93 94
#> gene_3 103 80 102 98 85 119
#> gene_9 108 103 124 95 92 104
#> gene_89 99 77 99 112 105 119
#> gene_51 89 101 106 94 109 102
#> gene_59 69 90 100 98 90 96
#> gene_52 85 103 103 121 98 93
#>