embed函数 R语言 多组样本的N种组合对于单个基因在多个样本组中的差异表达,通常使用方差分析,即,将多个组比较在一起以获得P值。如果p
embedå½æ° Rè¯è¨ å¤ç»æ ·æ¬çNç§ç»å
对äºå个åºå å¨å¤ä¸ªæ ·æ¬ç»ä¸çå·®å¼è¡¨è¾¾ï¼é常使ç¨æ¹å·®åæï¼å³ï¼å°å¤ä¸ªç»æ¯è¾å¨ä¸èµ·ä»¥è·å¾På¼ãå¦æpå¼æ¾èï¼è¯´æå¤ç»åºå 表达ææ¾èå·®å¼ãç¶èï¼æ们ä¸è½ç¥é两ç»ä¹é´æ两ç»ä¹é´çåºå 表达æ¯å¦ææ¾çæ§å·®å¼ï¼å æ¤æ们éè¦ç»ååç»ï¼æ¤æ¶ï¼æ们éè¦ä½¿ç¨æååç»åï¼
å¨Rè¯è¨ä¸ï¼å¯ä»¥ä½¿ç¨ combnï¼ï¼ å½æ°ä»ä¸ä¸ªåéä¸è·å¾ææå¯è½çå ç´ ç»åï¼
(All combinations of X elements of M are generated at one time).
ä¾å¦ï¼æ们ç°å¨æ4ç§Stageåæï¼ç°å¨è¦å¾å°ææå¯è½ç两两ç»åï¼ä»¥è¿è¡å·®å¼è¡¨è¾¾åæï¼
labels = c3I“, “II“, “III“, “IV“ï¼
res = tï¼combnï¼labels, 2ï¼ï¼
res
[,1] [,2]
[1,] “I“ “II“
[2,] “I“ “III“
[3,] “I“ “IV“
[4,] “II“ “III“
[5,] “II“ “IV“
[6,] “III“ “IV“
å¯è§ï¼ä¸¤ä¸¤ä¸ç»å ±æ6ç§å¯è½ï¼éè¦å¨æ¯ç§å¯è½çç»åå è¿è¡ä¸¤ç»é´å·®å¼è¡¨åæï¼å¦ææ¤æ¶ä½ å·²ç»å好äºä¸ä¸ªå为 limma_deaï¼ï¼ çå·®å¼è¡¨è¾¾åæå½æ°ï¼åå¯ä»¥å¾æ¹ä¾¿çå¨ combn å é¨è°ç¨è¯¥å½æ°ï¼
combnï¼labels, 2, FUN = limma_deaï¼
å¦æåªæ³åæä½ä¸å ¶ç¸é»ä¸ä¸ä½çç»åï¼
p_loadï¼gtoolsï¼
index = combinationsï¼lengthï¼labelsï¼, 2ï¼ ï¼ è¿åçæ¯ä¸æ
res[index[,2] == index[,1]+1,] ï¼ åºäºæ»¡è¶³æ¡ä»¶çä¸æ ååæ°æ®åé
[,1] [,2]
[1,] “I“ “II“
[2,] “II“ “III“
[3,] “III“ “IV“
ä¸è¿ï¼ææ´å ç®åçå®ç°æ¹å¼ï¼ embed å½æ°ï¼
Results each row of the matrix consists of sequences x [t] and x [t-1]...,
X [t-dimension + 1],
where t is the original index
of X.
comps = embedï¼labels,2ï¼[,2:1]
ä½æ¯ï¼ç±äº embed 没æè°ç¨å½æ°çæ¥å£ï¼æ以å¯ä»¥ä½¿ç¨ lapply å½æ°ï¼
my_comparisons = lapplyï¼1:nrowï¼compsï¼, functionï¼xï¼ comps[x,]ï¼
lapplyï¼my_comparisons, limma_deaï¼
ï¼ æè
lapplyï¼splitï¼comps, 1:nrowï¼compsï¼ï¼, limma_deaï¼