{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "Variables and assignments" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "a <- 1" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "1" ], "text/latex": [ "1" ], "text/markdown": [ "1" ], "text/plain": [ "[1] 1" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "a" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "a=13" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "13" ], "text/latex": [ "13" ], "text/markdown": [ "13" ], "text/plain": [ "[1] 13" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "a" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "R is a good tool to work with data vectors" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "v1 <- c(1,3,5,6,8)" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "?c" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "v2 <- 4:8" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 4
  2. 5
  3. 6
  4. 7
  5. 8
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 4\n", "\\item 5\n", "\\item 6\n", "\\item 7\n", "\\item 8\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 4\n", "2. 5\n", "3. 6\n", "4. 7\n", "5. 8\n", "\n", "\n" ], "text/plain": [ "[1] 4 5 6 7 8" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "v2" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [], "source": [ "v3 <- rep(0,5)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 0
  2. 0
  3. 0
  4. 0
  5. 0
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 0\n", "\\item 0\n", "\\item 0\n", "\\item 0\n", "\\item 0\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 0\n", "2. 0\n", "3. 0\n", "4. 0\n", "5. 0\n", "\n", "\n" ], "text/plain": [ "[1] 0 0 0 0 0" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "v3" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "You can do then various vector operations" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 5
  2. 6
  3. 7
  4. 8
  5. 9
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 5\n", "\\item 6\n", "\\item 7\n", "\\item 8\n", "\\item 9\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 5\n", "2. 6\n", "3. 7\n", "4. 8\n", "5. 9\n", "\n", "\n" ], "text/plain": [ "[1] 5 6 7 8 9" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "v2 + 1" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 12
  2. 15
  3. 18
  4. 21
  5. 24
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 12\n", "\\item 15\n", "\\item 18\n", "\\item 21\n", "\\item 24\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 12\n", "2. 15\n", "3. 18\n", "4. 21\n", "5. 24\n", "\n", "\n" ], "text/plain": [ "[1] 12 15 18 21 24" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "v2 * 3" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "One can combine vectors into matrices" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 'matrix'
  2. 'array'
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 'matrix'\n", "\\item 'array'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 'matrix'\n", "2. 'array'\n", "\n", "\n" ], "text/plain": [ "[1] \"matrix\" \"array\" " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "\n", "m1 <- cbind(v1,v2,v3)\n", "class(m1)" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "data": { "text/html": [ "5" ], "text/latex": [ "5" ], "text/markdown": [ "5" ], "text/plain": [ "[1] 5" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "
  1. 5
  2. 3
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 5\n", "\\item 3\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 5\n", "2. 3\n", "\n", "\n" ], "text/plain": [ "[1] 5 3" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "length(v2)\n", "dim(m1)" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [], "source": [ "m2 <- rbind(v1,v2,v3)" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 3 × 5 of type dbl
v113568
v245678
v300000
\n" ], "text/latex": [ "A matrix: 3 × 5 of type dbl\n", "\\begin{tabular}{r|lllll}\n", "\tv1 & 1 & 3 & 5 & 6 & 8\\\\\n", "\tv2 & 4 & 5 & 6 & 7 & 8\\\\\n", "\tv3 & 0 & 0 & 0 & 0 & 0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 3 × 5 of type dbl\n", "\n", "| v1 | 1 | 3 | 5 | 6 | 8 |\n", "| v2 | 4 | 5 | 6 | 7 | 8 |\n", "| v3 | 0 | 0 | 0 | 0 | 0 |\n", "\n" ], "text/plain": [ " [,1] [,2] [,3] [,4] [,5]\n", "v1 1 3 5 6 8 \n", "v2 4 5 6 7 8 \n", "v3 0 0 0 0 0 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "m2" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 5 × 3 of type dbl
v1v2v3
140
350
560
670
880
\n" ], "text/latex": [ "A matrix: 5 × 3 of type dbl\n", "\\begin{tabular}{lll}\n", " v1 & v2 & v3\\\\\n", "\\hline\n", "\t 1 & 4 & 0\\\\\n", "\t 3 & 5 & 0\\\\\n", "\t 5 & 6 & 0\\\\\n", "\t 6 & 7 & 0\\\\\n", "\t 8 & 8 & 0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 5 × 3 of type dbl\n", "\n", "| v1 | v2 | v3 |\n", "|---|---|---|\n", "| 1 | 4 | 0 |\n", "| 3 | 5 | 0 |\n", "| 5 | 6 | 0 |\n", "| 6 | 7 | 0 |\n", "| 8 | 8 | 0 |\n", "\n" ], "text/plain": [ " v1 v2 v3\n", "[1,] 1 4 0 \n", "[2,] 3 5 0 \n", "[3,] 5 6 0 \n", "[4,] 6 7 0 \n", "[5,] 8 8 0 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "m1" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Matrices operations can be done, eg. multiplication" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 5 × 5 of type dbl
172329 34 40
233445 53 64
294561 72 88
345372 85104
406488104128
\n" ], "text/latex": [ "A matrix: 5 × 5 of type dbl\n", "\\begin{tabular}{lllll}\n", "\t 17 & 23 & 29 & 34 & 40\\\\\n", "\t 23 & 34 & 45 & 53 & 64\\\\\n", "\t 29 & 45 & 61 & 72 & 88\\\\\n", "\t 34 & 53 & 72 & 85 & 104\\\\\n", "\t 40 & 64 & 88 & 104 & 128\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 5 × 5 of type dbl\n", "\n", "| 17 | 23 | 29 | 34 | 40 |\n", "| 23 | 34 | 45 | 53 | 64 |\n", "| 29 | 45 | 61 | 72 | 88 |\n", "| 34 | 53 | 72 | 85 | 104 |\n", "| 40 | 64 | 88 | 104 | 128 |\n", "\n" ], "text/plain": [ " [,1] [,2] [,3] [,4] [,5]\n", "[1,] 17 23 29 34 40 \n", "[2,] 23 34 45 53 64 \n", "[3,] 29 45 61 72 88 \n", "[4,] 34 53 72 85 104 \n", "[5,] 40 64 88 104 128 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "m1 %*% m2" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Matrices are indexed to get the rows, columns and cells by coordinates" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 3 × 3 of type dbl
v1v2v3
140
560
670
\n" ], "text/latex": [ "A matrix: 3 × 3 of type dbl\n", "\\begin{tabular}{lll}\n", " v1 & v2 & v3\\\\\n", "\\hline\n", "\t 1 & 4 & 0\\\\\n", "\t 5 & 6 & 0\\\\\n", "\t 6 & 7 & 0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 3 × 3 of type dbl\n", "\n", "| v1 | v2 | v3 |\n", "|---|---|---|\n", "| 1 | 4 | 0 |\n", "| 5 | 6 | 0 |\n", "| 6 | 7 | 0 |\n", "\n" ], "text/plain": [ " v1 v2 v3\n", "[1,] 1 4 0 \n", "[2,] 5 6 0 \n", "[3,] 6 7 0 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "m1[c(1,3,4),]" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\t\n", "\n", "
A matrix: 2 × 4 of type dbl
v11356
v24567
\n" ], "text/latex": [ "A matrix: 2 × 4 of type dbl\n", "\\begin{tabular}{r|llll}\n", "\tv1 & 1 & 3 & 5 & 6\\\\\n", "\tv2 & 4 & 5 & 6 & 7\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 2 × 4 of type dbl\n", "\n", "| v1 | 1 | 3 | 5 | 6 |\n", "| v2 | 4 | 5 | 6 | 7 |\n", "\n" ], "text/plain": [ " [,1] [,2] [,3] [,4]\n", "v1 1 3 5 6 \n", "v2 4 5 6 7 " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "\n", "
  1. 5
  2. 3
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 5\n", "\\item 3\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 5\n", "2. 3\n", "\n", "\n" ], "text/plain": [ "[1] 5 3" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "t(m1[1:4, 1:2])\n", "dim(m1)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "How big is the matrix? Dimensions..." ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\n", "
A matrix: 2 × 7 of type dbl
used(Mb)gc trigger(Mb)limit (Mb)max used(Mb)
Ncells 60955532.6121009864.7 NA121009864.7
Vcells1150634 8.8838860864.016384183892914.1
\n" ], "text/latex": [ "A matrix: 2 × 7 of type dbl\n", "\\begin{tabular}{r|lllllll}\n", " & used & (Mb) & gc trigger & (Mb) & limit (Mb) & max used & (Mb)\\\\\n", "\\hline\n", "\tNcells & 609555 & 32.6 & 1210098 & 64.7 & NA & 1210098 & 64.7\\\\\n", "\tVcells & 1150634 & 8.8 & 8388608 & 64.0 & 16384 & 1838929 & 14.1\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 2 × 7 of type dbl\n", "\n", "| | used | (Mb) | gc trigger | (Mb) | limit (Mb) | max used | (Mb) |\n", "|---|---|---|---|---|---|---|---|\n", "| Ncells | 609555 | 32.6 | 1210098 | 64.7 | NA | 1210098 | 64.7 |\n", "| Vcells | 1150634 | 8.8 | 8388608 | 64.0 | 16384 | 1838929 | 14.1 |\n", "\n" ], "text/plain": [ " used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)\n", "Ncells 609555 32.6 1210098 64.7 NA 1210098 64.7\n", "Vcells 1150634 8.8 8388608 64.0 16384 1838929 14.1" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "rm(m1)\n", "gc()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "More complex objects - lists" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [], "source": [ "l1 <- list()" ] }, { "cell_type": "code", "execution_count": 27, "metadata": {}, "outputs": [], "source": [ "l1[[1]] <- m1" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
    \n", "\t
  1. \n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
    A matrix: 5 × 3 of type dbl
    v1v2v3
    140
    350
    560
    670
    880
    \n", "
  2. \n", "
\n" ], "text/latex": [ "\\begin{enumerate}\n", "\\item A matrix: 5 × 3 of type dbl\n", "\\begin{tabular}{lll}\n", " v1 & v2 & v3\\\\\n", "\\hline\n", "\t 1 & 4 & 0\\\\\n", "\t 3 & 5 & 0\\\\\n", "\t 5 & 6 & 0\\\\\n", "\t 6 & 7 & 0\\\\\n", "\t 8 & 8 & 0\\\\\n", "\\end{tabular}\n", "\n", "\\end{enumerate}\n" ], "text/markdown": [ "1. \n", "A matrix: 5 × 3 of type dbl\n", "\n", "| v1 | v2 | v3 |\n", "|---|---|---|\n", "| 1 | 4 | 0 |\n", "| 3 | 5 | 0 |\n", "| 5 | 6 | 0 |\n", "| 6 | 7 | 0 |\n", "| 8 | 8 | 0 |\n", "\n", "\n", "\n", "\n" ], "text/plain": [ "[[1]]\n", " v1 v2 v3\n", "[1,] 1 4 0\n", "[2,] 3 5 0\n", "[3,] 5 6 0\n", "[4,] 6 7 0\n", "[5,] 8 8 0\n" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "l1" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [], "source": [ "l1[[2]] <- v2" ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
    \n", "\t
  1. \n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
    A matrix: 5 × 3 of type dbl
    v1v2v3
    140
    350
    560
    670
    880
    \n", "
  2. \n", "\t
  3. \n", "
    1. 4
    2. 5
    3. 6
    4. 7
    5. 8
    \n", "
  4. \n", "
\n" ], "text/latex": [ "\\begin{enumerate}\n", "\\item A matrix: 5 × 3 of type dbl\n", "\\begin{tabular}{lll}\n", " v1 & v2 & v3\\\\\n", "\\hline\n", "\t 1 & 4 & 0\\\\\n", "\t 3 & 5 & 0\\\\\n", "\t 5 & 6 & 0\\\\\n", "\t 6 & 7 & 0\\\\\n", "\t 8 & 8 & 0\\\\\n", "\\end{tabular}\n", "\n", "\\item \\begin{enumerate*}\n", "\\item 4\n", "\\item 5\n", "\\item 6\n", "\\item 7\n", "\\item 8\n", "\\end{enumerate*}\n", "\n", "\\end{enumerate}\n" ], "text/markdown": [ "1. \n", "A matrix: 5 × 3 of type dbl\n", "\n", "| v1 | v2 | v3 |\n", "|---|---|---|\n", "| 1 | 4 | 0 |\n", "| 3 | 5 | 0 |\n", "| 5 | 6 | 0 |\n", "| 6 | 7 | 0 |\n", "| 8 | 8 | 0 |\n", "\n", "\n", "2. 1. 4\n", "2. 5\n", "3. 6\n", "4. 7\n", "5. 8\n", "\n", "\n", "\n", "\n", "\n" ], "text/plain": [ "[[1]]\n", " v1 v2 v3\n", "[1,] 1 4 0\n", "[2,] 3 5 0\n", "[3,] 5 6 0\n", "[4,] 6 7 0\n", "[5,] 8 8 0\n", "\n", "[[2]]\n", "[1] 4 5 6 7 8\n" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "l1" ] }, { "cell_type": "code", "execution_count": 31, "metadata": {}, "outputs": [], "source": [ "l1$description <- \"turlututu\"" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\t
[[1]]
\n", "\t\t
\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 5 × 3 of type dbl
v1v2v3
140
350
560
670
880
\n", "
\n", "\t
[[2]]
\n", "\t\t
\n", "
  1. 4
  2. 5
  3. 6
  4. 7
  5. 8
\n", "
\n", "\t
$description
\n", "\t\t
'turlututu'
\n", "
\n" ], "text/latex": [ "\\begin{description}\n", "\\item[{[[1]]}] A matrix: 5 × 3 of type dbl\n", "\\begin{tabular}{lll}\n", " v1 & v2 & v3\\\\\n", "\\hline\n", "\t 1 & 4 & 0\\\\\n", "\t 3 & 5 & 0\\\\\n", "\t 5 & 6 & 0\\\\\n", "\t 6 & 7 & 0\\\\\n", "\t 8 & 8 & 0\\\\\n", "\\end{tabular}\n", "\n", "\\item[{[[2]]}] \\begin{enumerate*}\n", "\\item 4\n", "\\item 5\n", "\\item 6\n", "\\item 7\n", "\\item 8\n", "\\end{enumerate*}\n", "\n", "\\item[\\$description] 'turlututu'\n", "\\end{description}\n" ], "text/markdown": [ "[[1]]\n", ": \n", "A matrix: 5 × 3 of type dbl\n", "\n", "| v1 | v2 | v3 |\n", "|---|---|---|\n", "| 1 | 4 | 0 |\n", "| 3 | 5 | 0 |\n", "| 5 | 6 | 0 |\n", "| 6 | 7 | 0 |\n", "| 8 | 8 | 0 |\n", "\n", "\n", "[[2]]\n", ": 1. 4\n", "2. 5\n", "3. 6\n", "4. 7\n", "5. 8\n", "\n", "\n", "\n", "$description\n", ": 'turlututu'\n", "\n", "\n" ], "text/plain": [ "[[1]]\n", " v1 v2 v3\n", "[1,] 1 4 0\n", "[2,] 3 5 0\n", "[3,] 5 6 0\n", "[4,] 6 7 0\n", "[5,] 8 8 0\n", "\n", "[[2]]\n", "[1] 4 5 6 7 8\n", "\n", "$description\n", "[1] \"turlututu\"\n" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "l1" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "More complex objects" ] }, { "cell_type": "code", "execution_count": 33, "metadata": {}, "outputs": [], "source": [ "load(\"DEGlist.Rd\")" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 'a'
  2. 'l1'
  3. 'm1'
  4. 'm2'
  5. 'v1'
  6. 'v2'
  7. 'v3'
  8. 'y'
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 'a'\n", "\\item 'l1'\n", "\\item 'm1'\n", "\\item 'm2'\n", "\\item 'v1'\n", "\\item 'v2'\n", "\\item 'v3'\n", "\\item 'y'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 'a'\n", "2. 'l1'\n", "3. 'm1'\n", "4. 'm2'\n", "5. 'v1'\n", "6. 'v2'\n", "7. 'v3'\n", "8. 'y'\n", "\n", "\n" ], "text/plain": [ "[1] \"a\" \"l1\" \"m1\" \"m2\" \"v1\" \"v2\" \"v3\" \"y\" " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "'DGEList'" ], "text/latex": [ "'DGEList'" ], "text/markdown": [ "'DGEList'" ], "text/plain": [ "[1] \"DGEList\"\n", "attr(,\"package\")\n", "[1] \"edgeR\"" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "ls()\n", "class(y)" ] }, { "cell_type": "code", "execution_count": 35, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Loading required package: edgeR\n", "\n", "Loading required package: limma\n", "\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Formal class 'DGEList' [package \"edgeR\"] with 1 slot\n", " ..@ .Data:List of 11\n", " .. ..$ : int [1:57992, 1:6] 11 2089 0 2 0 0 0 0 45 0 ...\n", " .. .. ..- attr(*, \"dimnames\")=List of 2\n", " .. .. .. ..$ : chr [1:57992] \"ENSG00000223972\" \"ENSG00000227232\" \"ENSG00000278267\" \"ENSG00000243485\" ...\n", " .. .. .. ..$ : chr [1:6] \"mfc_cnt_1\" \"mfc_cnt_2\" \"mfc_cnt_3\" \"mfc_dac_1\" ...\n", " .. ..$ :'data.frame':\t6 obs. of 3 variables:\n", " .. .. ..$ group : Factor w/ 2 levels \"1\",\"2\": 1 1 1 2 2 2\n", " .. .. ..$ lib.size : num [1:6] 22230293 30709932 88453516 41361601 44072270 ...\n", " .. .. ..$ norm.factors: num [1:6] 1.001 0.953 0.918 1.063 1.057 ...\n", " .. ..$ : num [1:6, 1:2] 1 1 1 1 1 1 0 0 0 1 ...\n", " .. .. ..- attr(*, \"dimnames\")=List of 2\n", " .. .. .. ..$ : chr [1:6] \"1\" \"2\" \"3\" \"4\" ...\n", " .. .. .. ..$ : chr [1:2] \"(Intercept)\" \"group2\"\n", " .. .. ..- attr(*, \"assign\")= int [1:2] 0 1\n", " .. .. ..- attr(*, \"contrasts\")=List of 1\n", " .. .. .. ..$ group: chr \"contr.treatment\"\n", " .. ..$ : num 0.0124\n", " .. ..$ : num [1:57992] 0.01991 0.00938 0.05591 0.03574 0.05591 ...\n", " .. ..$ : num [1:57992] 0.01183 0.00767 0.05591 0.00734 0.05591 ...\n", " .. ..$ : num [1:57992] -0.106 6.458 -4.516 -2.264 -4.516 ...\n", " .. ..$ : chr \"locfit\"\n", " .. ..$ : num 12.6\n", " .. ..$ : num 3.16\n", " .. ..$ : num 0.28\n" ] } ], "source": [ "str(y)" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\t\n", "\n", "\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\t\n", "\n", "
A matrix: 10 × 6 of type int
mfc_cnt_1mfc_cnt_2mfc_cnt_3mfc_dac_1mfc_dac_2mfc_dac_3
ENSG00000223972 11 18 55 46 57 56
ENSG00000227232208924417559364441724329
ENSG00000278267 0 0 0 0 0 0
ENSG00000243485 2 3 8 8 11 13
ENSG00000237613 0 0 0 0 0 0
ENSG00000268020 0 0 0 0 0 0
ENSG00000240361 0 0 0 0 0 0
ENSG00000186092 0 0 0 0 0 0
ENSG00000238009 45 80 183 110 111 122
ENSG00000239945 0 0 0 0 0 0
\n" ], "text/latex": [ "A matrix: 10 × 6 of type int\n", "\\begin{tabular}{r|llllll}\n", " & mfc\\_cnt\\_1 & mfc\\_cnt\\_2 & mfc\\_cnt\\_3 & mfc\\_dac\\_1 & mfc\\_dac\\_2 & mfc\\_dac\\_3\\\\\n", "\\hline\n", "\tENSG00000223972 & 11 & 18 & 55 & 46 & 57 & 56\\\\\n", "\tENSG00000227232 & 2089 & 2441 & 7559 & 3644 & 4172 & 4329\\\\\n", "\tENSG00000278267 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000243485 & 2 & 3 & 8 & 8 & 11 & 13\\\\\n", "\tENSG00000237613 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000268020 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000240361 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000186092 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\tENSG00000238009 & 45 & 80 & 183 & 110 & 111 & 122\\\\\n", "\tENSG00000239945 & 0 & 0 & 0 & 0 & 0 & 0\\\\\n", "\\end{tabular}\n" ], "text/markdown": [ "\n", "A matrix: 10 × 6 of type int\n", "\n", "| | mfc_cnt_1 | mfc_cnt_2 | mfc_cnt_3 | mfc_dac_1 | mfc_dac_2 | mfc_dac_3 |\n", "|---|---|---|---|---|---|---|\n", "| ENSG00000223972 | 11 | 18 | 55 | 46 | 57 | 56 |\n", "| ENSG00000227232 | 2089 | 2441 | 7559 | 3644 | 4172 | 4329 |\n", "| ENSG00000278267 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000243485 | 2 | 3 | 8 | 8 | 11 | 13 |\n", "| ENSG00000237613 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000268020 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000240361 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000186092 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "| ENSG00000238009 | 45 | 80 | 183 | 110 | 111 | 122 |\n", "| ENSG00000239945 | 0 | 0 | 0 | 0 | 0 | 0 |\n", "\n" ], "text/plain": [ " mfc_cnt_1 mfc_cnt_2 mfc_cnt_3 mfc_dac_1 mfc_dac_2 mfc_dac_3\n", "ENSG00000223972 11 18 55 46 57 56 \n", "ENSG00000227232 2089 2441 7559 3644 4172 4329 \n", "ENSG00000278267 0 0 0 0 0 0 \n", "ENSG00000243485 2 3 8 8 11 13 \n", "ENSG00000237613 0 0 0 0 0 0 \n", "ENSG00000268020 0 0 0 0 0 0 \n", "ENSG00000240361 0 0 0 0 0 0 \n", "ENSG00000186092 0 0 0 0 0 0 \n", "ENSG00000238009 45 80 183 110 111 122 \n", "ENSG00000239945 0 0 0 0 0 0 " ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "y@.Data[[1]][1:10, 1:6]" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\t
$names
\n", "\t\t
\n", "
  1. 'counts'
  2. 'samples'
  3. 'design'
  4. 'common.dispersion'
  5. 'trended.dispersion'
  6. 'tagwise.dispersion'
  7. 'AveLogCPM'
  8. 'trend.method'
  9. 'prior.df'
  10. 'prior.n'
  11. 'span'
\n", "
\n", "\t
$class
\n", "\t\t
'DGEList'
\n", "
\n" ], "text/latex": [ "\\begin{description}\n", "\\item[\\$names] \\begin{enumerate*}\n", "\\item 'counts'\n", "\\item 'samples'\n", "\\item 'design'\n", "\\item 'common.dispersion'\n", "\\item 'trended.dispersion'\n", "\\item 'tagwise.dispersion'\n", "\\item 'AveLogCPM'\n", "\\item 'trend.method'\n", "\\item 'prior.df'\n", "\\item 'prior.n'\n", "\\item 'span'\n", "\\end{enumerate*}\n", "\n", "\\item[\\$class] 'DGEList'\n", "\\end{description}\n" ], "text/markdown": [ "$names\n", ": 1. 'counts'\n", "2. 'samples'\n", "3. 'design'\n", "4. 'common.dispersion'\n", "5. 'trended.dispersion'\n", "6. 'tagwise.dispersion'\n", "7. 'AveLogCPM'\n", "8. 'trend.method'\n", "9. 'prior.df'\n", "10. 'prior.n'\n", "11. 'span'\n", "\n", "\n", "\n", "$class\n", ": 'DGEList'\n", "\n", "\n" ], "text/plain": [ "$names\n", " [1] \"counts\" \"samples\" \"design\" \n", " [4] \"common.dispersion\" \"trended.dispersion\" \"tagwise.dispersion\"\n", " [7] \"AveLogCPM\" \"trend.method\" \"prior.df\" \n", "[10] \"prior.n\" \"span\" \n", "\n", "$class\n", "[1] \"DGEList\"\n", "attr(,\"package\")\n", "[1] \"edgeR\"\n" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "attributes(y)" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "data": { "text/html": [ "'factor'" ], "text/latex": [ "'factor'" ], "text/markdown": [ "'factor'" ], "text/plain": [ "[1] \"factor\"" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "class(y$samples[,1])\n" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. 1
  2. 1
  3. 1
  4. 2
  5. 2
  6. 2
\n", "\n", "
\n", "\t\n", "\t\tLevels:\n", "\t\n", "\t\n", "\t
  1. '1'
  2. '2'
\n", "
" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item 1\n", "\\item 1\n", "\\item 1\n", "\\item 2\n", "\\item 2\n", "\\item 2\n", "\\end{enumerate*}\n", "\n", "\\emph{Levels}: \\begin{enumerate*}\n", "\\item '1'\n", "\\item '2'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. 1\n", "2. 1\n", "3. 1\n", "4. 2\n", "5. 2\n", "6. 2\n", "\n", "\n", "\n", "**Levels**: 1. '1'\n", "2. '2'\n", "\n", "\n" ], "text/plain": [ "[1] 1 1 1 2 2 2\n", "Levels: 1 2" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "y$samples[,1]\n" ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "
  1. '1'
  2. '2'
\n" ], "text/latex": [ "\\begin{enumerate*}\n", "\\item '1'\n", "\\item '2'\n", "\\end{enumerate*}\n" ], "text/markdown": [ "1. '1'\n", "2. '2'\n", "\n", "\n" ], "text/plain": [ "[1] \"1\" \"2\"" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "levels(y$samples[,1])" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "R", "language": "R", "name": "ir" }, "language_info": { "codemirror_mode": "r", "file_extension": ".r", "mimetype": "text/x-r-source", "name": "R", "pygments_lexer": "r", "version": "4.0.3" } }, "nbformat": 4, "nbformat_minor": 2 }