Reduces a assay to a representative matrix
reduce_cpgs( scm, assay = "score", var = c("top", "rand"), top_var = 1000, na.rm = FALSE, verbose = FALSE )
| scm | scMethrix; Input |
|---|---|
| assay | string; The assay to use. Default is 'score' |
| var | strning; Choose between random CpG sites ('rand') or most variable CpGs ('top'). Default 'top' |
| top_var | integer; Number of variable CpGs to use. Default 1000 Set it to NULL to use all CpGs (which is not recommended due to memory requirements). |
| na.rm | boolean; flag to remove NA values |
| verbose | boolean; flag to output messages or not |
matrix; the reduced form of the input assay
For the purposes of dimensionality reduction, this function selects either random CpGs or those with the highest variability.
#>#> C1 C2 C3 C4 #> [1,] NA 0.0 1.0 NA #> [2,] NA NA 1.0 0.0 #> [3,] 0.0 NA NA 1.0 #> [4,] 0.0 NA NA 1.0 #> [5,] NA NA 1.0 0.0 #> [6,] NA 1.0 0.0 NA #> [7,] 0.0 1.0 NA NA #> [8,] NA 1.0 NA 0.0 #> [9,] 1.0 NA NA 0.0 #> [10,] 0.0 NA 1.0 NA #> [11,] 0.0 NA NA 1.0 #> [12,] 0.0 NA NA 1.0 #> [13,] NA 1.0 NA 0.0 #> [14,] 1.0 NA 1.0 0.0 #> [15,] 0.0 1.0 0.0 NA #> [16,] NA 1.0 1.0 0.0 #> [17,] NA 0.0 1.0 1.0 #> [18,] 1.0 1.0 NA 0.0 #> [19,] 1.0 NA 0.0 1.0 #> [20,] 1.0 1.0 NA 0.0 #> [21,] NA 1.0 0.0 1.0 #> [22,] 1.0 0.0 NA 0.0 #> [23,] 1.0 NA 0.0 0.0 #> [24,] NA 1.0 0.0 1.0 #> [25,] 1.0 1.0 NA 0.0 #> [26,] 0.0 1.0 NA 0.0 #> [27,] NA 1.0 1.0 0.0 #> [28,] 0.0 1.0 1.0 NA #> [29,] 0.0 1.0 NA 1.0 #> [30,] 1.0 1.0 0.0 NA #> [31,] 1.0 1.0 0.0 0.0 #> [32,] 0.0 1.0 1.0 0.0 #> [33,] 0.0 1.0 0.0 1.0 #> [34,] 0.0 1.0 1.0 0.0 #> [35,] 1.0 1.0 0.0 0.0 #> [36,] 1.0 1.0 0.0 0.0 #> [37,] 1.0 0.0 1.0 0.0 #> [38,] 1.0 0.0 1.0 1.0 #> [39,] 1.0 1.0 1.0 0.0 #> [40,] NA 1.0 0.0 0.5 #> [41,] 0.0 0.0 0.0 1.0 #> [42,] 1.0 0.0 1.0 1.0 #> [43,] 1.0 1.0 0.0 1.0 #> [44,] 1.0 0.0 1.0 1.0 #> [45,] 1.0 0.0 1.0 1.0 #> [46,] 1.0 0.0 1.0 1.0 #> [47,] 0.0 1.0 1.0 1.0 #> [48,] 0.0 1.0 1.0 1.0 #> [49,] 0.0 0.0 0.0 1.0 #> [50,] NA 1.0 0.5 0.0 #> [51,] 1.0 0.0 0.0 0.0 #> [52,] 1.0 0.0 1.0 1.0 #> [53,] 1.0 0.0 0.0 0.0 #> [54,] 0.0 0.0 1.0 0.0 #> [55,] 1.0 0.5 0.0 0.0 #> [56,] 0.5 NA 1.0 NA #> [57,] NA NA 1.0 0.5 #> [58,] 0.5 0.0 NA 0.0 #> [59,] 1.0 NA 1.0 0.5 #> [60,] 0.5 0.5 1.0 NA #> [61,] 0.0 0.0 0.5 0.0 #> [62,] 1.0 1.0 1.0 NA #> [63,] NA 1.0 NA 1.0 #> [64,] NA 1.0 1.0 1.0 #> [65,] 0.0 NA 0.0 0.0 #> [66,] NA 1.0 1.0 NA #> [67,] 1.0 1.0 NA NA #> [68,] 1.0 1.0 1.0 NA #> [69,] 1.0 1.0 1.0 NA #> [70,] 1.0 1.0 1.0 1.0 #> [71,] 1.0 1.0 NA 1.0 #> [72,] NA NA 1.0 1.0 #> [73,] 1.0 NA 1.0 1.0 #> [74,] 1.0 NA 1.0 1.0 #> [75,] 1.0 NA 1.0 1.0 #> [76,] 1.0 1.0 1.0 NA #> [77,] 0.0 NA 0.0 0.0 #> [78,] 1.0 1.0 1.0 NA #> [79,] 1.0 1.0 1.0 NA #> [80,] 0.0 0.0 0.0 0.0 #> [81,] 1.0 NA 1.0 NA #> [82,] 1.0 1.0 1.0 1.0 #> [83,] 0.0 NA 0.0 0.0 #> [84,] 1.0 1.0 1.0 1.0 #> [85,] NA NA 1.0 1.0 #> [86,] 1.0 NA 1.0 NA #> [87,] 1.0 NA 1.0 1.0 #> [88,] 1.0 NA NA 1.0 #> [89,] NA 1.0 NA 1.0 #> [90,] 0.0 0.0 0.0 0.0 #> [91,] 1.0 NA 1.0 1.0 #> [92,] 0.0 NA 0.0 NA #> [93,] 1.0 NA 1.0 1.0 #> [94,] NA 1.0 1.0 NA #> [95,] 1.0 1.0 1.0 1.0 #> [96,] NA NA 1.0 1.0 #> [97,] NA 1.0 NA 1.0 #> [98,] NA NA 1.0 1.0 #> [99,] 1.0 1.0 NA 1.0 #> [100,] 1.0 1.0 1.0 1.0 #> [101,] 1.0 1.0 NA NA #> [102,] NA 0.0 0.0 0.0 #> [103,] 0.0 0.0 0.0 0.0 #> [104,] NA 0.0 0.0 0.0 #> [105,] 1.0 NA 1.0 1.0 #> [106,] 1.0 1.0 NA 1.0 #> [107,] 1.0 NA NA 1.0 #> [108,] NA 1.0 NA 1.0 #> [109,] 1.0 NA 1.0 NA #> [110,] 1.0 1.0 NA 1.0 #> [111,] 0.0 NA 0.0 NA #> [112,] NA 1.0 1.0 1.0 #> [113,] 1.0 NA 1.0 1.0 #> [114,] NA NA 1.0 1.0 #> [115,] 1.0 NA 1.0 1.0 #> [116,] NA 1.0 1.0 NA #> [117,] 1.0 NA 1.0 1.0 #> [118,] 1.0 NA NA 1.0 #> [119,] 0.0 0.0 0.0 0.0 #> [120,] 0.0 0.0 0.0 NA #> [121,] 1.0 NA 1.0 1.0 #> [122,] 0.0 NA 0.0 0.0 #> [123,] 1.0 1.0 1.0 1.0 #> [124,] 1.0 1.0 1.0 1.0 #> [125,] 1.0 1.0 1.0 1.0 #> [126,] NA 1.0 1.0 1.0 #> [127,] 0.0 0.0 NA NA #> [128,] 0.0 0.0 0.0 NA #> [129,] NA 1.0 1.0 1.0 #> [130,] 1.0 NA NA 1.0 #> [131,] NA NA 1.0 1.0 #> [132,] 0.0 0.0 NA NA #> [133,] 1.0 1.0 1.0 1.0 #> [134,] 1.0 1.0 NA 1.0 #> [135,] NA 1.0 1.0 1.0 #> [136,] 1.0 1.0 NA 1.0 #> [137,] NA NA 1.0 1.0 #> [138,] 0.0 0.0 NA NA #> [139,] 1.0 NA 1.0 1.0 #> [140,] 1.0 NA 1.0 NA #> [141,] 1.0 1.0 1.0 1.0 #> [142,] NA 1.0 1.0 NA #> [143,] NA 1.0 NA 1.0 #> [144,] 1.0 NA 1.0 1.0 #> [145,] NA 0.0 NA 0.0 #> [146,] 1.0 NA 1.0 1.0 #> [147,] NA NA 1.0 1.0 #> [148,] 1.0 1.0 NA 1.0 #> [149,] 1.0 1.0 NA 1.0 #> [150,] 1.0 NA 1.0 NA #> [151,] 1.0 1.0 1.0 NA #> [152,] 1.0 1.0 1.0 1.0 #> [153,] 1.0 1.0 1.0 1.0 #> [154,] NA 0.0 NA 0.0 #> [155,] 0.0 0.0 0.0 NA #> [156,] 1.0 1.0 1.0 1.0 #> [157,] 1.0 NA 1.0 1.0 #> [158,] 1.0 NA 1.0 NA #> [159,] NA 0.0 NA 0.0 #> [160,] 1.0 1.0 1.0 1.0 #> [161,] 0.0 NA 0.0 0.0 #> [162,] NA 1.0 1.0 1.0 #> [163,] NA 1.0 1.0 NA #> [164,] NA 1.0 NA 1.0 #> [165,] NA 1.0 NA 1.0 #> [166,] NA 1.0 NA 1.0 #> [167,] 0.0 0.0 0.0 0.0 #> [168,] NA NA 0.0 0.0 #> [169,] 0.0 0.0 0.0 0.0 #> [170,] 0.0 0.0 0.0 0.0 #> [171,] 0.0 0.0 0.0 0.0 #> [172,] 0.0 0.0 0.0 0.0 #> [173,] NA 1.0 1.0 NA #> [174,] 1.0 NA NA 1.0 #> [175,] 1.0 NA 1.0 NA #> [176,] 1.0 1.0 1.0 NA #> [177,] NA 1.0 1.0 1.0 #> [178,] NA 1.0 1.0 1.0 #> [179,] 1.0 1.0 1.0 1.0 #> [180,] 0.0 0.0 NA 0.0 #> [181,] 1.0 1.0 NA NA #> [182,] 1.0 NA NA 1.0 #> [183,] 1.0 1.0 1.0 1.0 #> [184,] 1.0 1.0 NA 1.0 #> [185,] 0.0 NA 0.0 NA #> [186,] 1.0 1.0 1.0 NA #> [187,] 1.0 1.0 1.0 NA #> [188,] NA 1.0 NA 1.0 #> [189,] 1.0 1.0 1.0 NA #> [190,] 1.0 1.0 1.0 1.0 #> [191,] NA NA 1.0 1.0 #> [192,] 1.0 1.0 NA 1.0 #> [193,] 1.0 1.0 1.0 1.0 #> [194,] 1.0 NA 1.0 1.0 #> [195,] NA NA 1.0 1.0 #> [196,] NA NA 1.0 1.0 #> [197,] NA 1.0 1.0 NA #> [198,] 1.0 1.0 1.0 NA #> [199,] 1.0 1.0 NA NA #> [200,] 1.0 NA 1.0 NA #> [201,] 1.0 1.0 1.0 NA #> [202,] 1.0 1.0 1.0 NA #> [203,] NA 1.0 1.0 NA #> [204,] NA 1.0 1.0 1.0 #> [205,] 1.0 1.0 1.0 1.0 #> [206,] 1.0 NA 1.0 1.0 #> [207,] 1.0 NA 1.0 1.0 #> [208,] 1.0 1.0 NA NA #> [209,] 1.0 1.0 NA 1.0 #> [210,] NA NA 0.0 0.0 #> [211,] 1.0 1.0 NA 1.0 #> [212,] 0.0 NA 0.0 0.0 #> [213,] 1.0 1.0 1.0 1.0 #> [214,] 0.0 0.0 0.0 0.0 #> [215,] 0.0 0.0 0.0 0.0 #> [216,] 0.0 0.0 0.0 0.0 #> [217,] 0.0 0.0 0.0 0.0 #> [218,] 0.0 0.0 0.0 0.0 #> [219,] 0.0 0.0 0.0 0.0 #> [220,] NA NA 1.0 NA #> [221,] 1.0 NA NA NA #> [222,] NA 1.0 NA NA #> [223,] NA 1.0 NA NA #> [224,] NA 1.0 NA NA #> [225,] 1.0 NA NA NA #> [226,] NA NA NA 1.0 #> [227,] NA NA 1.0 NA #> [228,] NA NA 0.0 NA #> [229,] 0.0 NA NA NA #> [230,] NA NA 1.0 NA #> [231,] 0.0 NA NA NA #> [232,] NA NA 1.0 NA #> [233,] NA NA 1.0 NA #> [234,] 1.0 NA NA NA #> [235,] 1.0 NA NA NA #> [236,] 1.0 NA NA NA #> [237,] NA NA 1.0 NA #> [238,] 0.0 NA NA NA #> [239,] NA NA 0.0 NA #> [240,] NA NA NA 1.0 #> [241,] NA NA 1.0 NA #> [242,] NA 1.0 NA NA #> [243,] NA NA NA 0.0 #> [244,] NA NA NA 1.0 #> [245,] NA NA NA 0.0 #> [246,] 1.0 NA NA NA #> [247,] NA NA 1.0 NA #> [248,] NA NA NA 1.0 #> [249,] NA NA 0.0 NA #> [250,] NA 1.0 NA NA #> [251,] 1.0 NA NA NA #> [252,] 1.0 NA NA NA #> [253,] 1.0 NA NA NA #> [254,] 1.0 NA NA NA #> [255,] NA 1.0 NA NA #> [256,] 0.0 NA NA NA #> [257,] NA NA 1.0 NA #> [258,] NA NA 0.0 NA #> [259,] NA NA 0.0 NA #> [260,] NA NA 1.0 NA #> [261,] 1.0 NA NA NA #> [262,] NA NA 0.0 NA #> [263,] NA 1.0 NA NA #> [264,] 0.0 NA NA NA #> [265,] NA 0.0 NA NA #> [266,] 1.0 NA NA NA #> [267,] NA NA NA 1.0 #> [268,] NA NA 1.0 NA #> [269,] NA NA NA 1.0 #> [270,] NA NA NA 1.0 #> [271,] NA NA 0.0 NA #> [272,] NA NA NA 1.0 #> [273,] NA NA 1.0 NA #> [274,] NA 1.0 NA NA #> [275,] NA 1.0 NA NA #> [276,] NA 1.0 NA NA #> [277,] NA NA 1.0 NA #> [278,] NA 1.0 NA NA #> [279,] 0.0 NA NA NA #> [280,] 1.0 NA NA NA #> [281,] NA NA NA 1.0 #> [282,] 1.0 NA NA NA #> [283,] NA NA 0.0 NA #> [284,] NA NA 1.0 NA #> [285,] NA NA NA 0.0 #> [286,] NA NA NA 0.0